Prabowo enrolled in Indonesia’s Military Academy in Magelang in 1970. He graduated in 1974 with others who would gain senior leadership positions such as Susilo Bambang Yudhoyono.

In 1976, Prabowo served in the Indonesian National Army Special Force Kopassus and was assigned as the commander of Group 1 Komando Pasukan Sandhi Yudha (Kopassandha), which was one of the Indonesian Army’s Nanggala commando units in East Timor, the former Portuguese territory that Indonesia had invaded the previous year. Prabowo, then 26 years old, was the youngest Nanggala commander. Prabowo led the mission to capture the vice president of Fretilin, who was the first Prime Minister of East Timor, Nicolau dos Reis Lobato. Guiding Prabowo was Antonio Lobato – Nicolau’s younger brother. On 31 December 1978, Prabowo’s company found and fatally shot Nicolau in the stomach as he was being escorted in Maubisse, fifty kilometres south of Dili.

Prabowo married Suharto’s daughter, Siti Hediati Hariyadi, in 1983. They have a son, Didit Hediprasetyo, who lived in Boston before settling in Paris to pursue a career in design.

In 1985 Prabowo attended the Advanced Infantry Officers Course at Fort Benning, in the United States for commando training. In the early 1990s, as the commander of Kopassus Group 3, the now Major General Prabowo attempted to crush the East Timorese independence movement by using irregular troops (hooded “ninja” gangs dressed in black and operating at night) and, in main towns and villages, militias trained and directed by Kopassus commanders. Human rights abuses rose. The Army’s 1997 campaign was called Operation Eradicate.

Prabowo rebranded Kiani Kertas to Kertas Nusantara. The company was established in 1990 and is part of the Nusantara Energy. It controls an area of 3,400 hectares used for paper mills, employee housing, private schools, and various company facilities. Kiani has been awarded ISO 900–2005 status as one of the highest quality management companies. It is reported that Kiani Kertas has been experiencing financial difficulties, and in early 2014, workers took to the streets to demand their wages which had not been paid in five months.

Using his connections to President Suharto, Prabowo and his brother worked to silence journalistic and political critics in the 1990s. Hashim unsuccessfully pressured Goenawan Mohamad to sell his outspoken and banned Tempo magazine to him. As a lieutenant colonel, Prabowo invited Gus Dur to his battalion headquarters in 1992 and warned him to stick to religion and to stay out of politics, or face unspecified actions if he continued to oppose the president. He later warned the intellectual Nurcholish Madjid (Cak Nur) to resign from the KIPP, the election monitoring unit set up by Goenawan Mohamad, which armed forces commander Feisal Tanjung had denounced as “obviously unconstitutional”.

In 1996, Prabowo led the Mapenduma Operation in the mountainous terrain of Papua, Indonesia. The goal of the operation was the release of 11 scientific researchers, who had been taken hostage by the Free Papua Movement (OPM). The researchers were five Indonesians, four Britons, one Dutchman and his pregnant German wife. Two of the Indonesian male hostages were killed shortly before the rescue operation. The mission involved covert support from British Military Attache and SAS veteran Colonel Ivor Helberg. Following the hostage transfer, Kopassus under Prabowo began a reprisal campaign against villages perceived to support OPM, in one incident at Geselema village attacking the villagers with a military helicopter disguised as a Red Cross helicopter.

On 20 March 1998, Prabowo was appointed head of the 27,000-strong Army Strategic Reserve Command (Kostrad), that Suharto had commanded in 1965.

On 21 May 1998, Suharto announced his resignation from the presidency and Vice President B. J. Habibie took over as president.

Following an ABRI investigation, Prabowo acknowledged responsibility for the kidnapping of the activists. He was discharged from military service in August. He and Wiranto denied that the discharge was a result of disciplinary action. In August 1998, the Dewan Kehormatan Perwira (Officers Council of Honor) tried and found Prabowo guilty of “misinterpreting orders” in the kidnapping of anti-Suharto activists in 1998. He was discharged from military services and went into a voluntary exile in Jordan where he knew that country’s new young King Abdullah as a fellow commander of special forces. In an interview with Asiaweek magazine in 2000, Prabowo said “I never threatened Habibie. I was not behind the riots. That is a great lie. I never betrayed Pak Harto. I never betrayed Habibie. I never betrayed my country…There was a certain group that wanted to make me a scapegoat, maybe to hide their involvement.”” Rights groups have long questioned Prabowo’s eligibility to run for president, noting that he was discharged dishonourably from the Army in August 1998 for “misinterpreting orders” in the abduction of the democracy activists. While that was the military’s official statement, observers have long believed that it was a coup conspiracy that saw Prabowo, then the commander of the Army Strategic Reserves, given his marching orders.

According to Douglas Ramage of the Jakarta-based Bower’s Asia Group, this was the first time since reformasi began in 1998 that the legitimacy of an election was questioned; he declared the country was entering “uncharted territory”. The legality of a Prabowo challenge is questionable, as – if he withdrew – he is no longer considered a presidential candidate. If he can make the challenge, according to The Jakarta Post, the gap between the two is sufficient to make such a challenge difficult. Under the presidential election law, Prabowo could face up to six years in prison and a 100 billion rupiah ($10 million) fine for withdrawing. Later that evening, Joko Widodo was officially announced as president and began to receive congratulations from world leaders.

In 2004, Prabowo was one of five contenders vying to become Golkar party’s presidential candidate. He received the lowest number of votes, just 39, and was eliminated in the first round. The second round of voting was won by Wiranto. In early 2008, Prabowo’s inner circle, including Fadli Zon, established the Great Indonesia Movement Party (Gerindra), which nominated Prabowo for the presidency in the 2009 elections. However, having won 26 out of 560 seats in the Indonesian parliament, the party did not have the required numbers, and Prabowo ran as a vice presidential candidate to Megawati Soekarnoputri, daughter of Indonesia’s first president Sukarno. The pair, referred to colloquially by the Indonesian media as Mega–Pro, earned 27% of the vote and lost to Susilo Bambang Yudhoyono and his running mate, economist Boediono.

In 2007, PT Ridlatama, whose majority stakeholder was British-based Churchill PLC, conducted a geo-survey eastern Kalimantan for coal. Two months after the survey yielded positive results, East Kutai officials granted mining licenses to Nusantara Energy (a subsidiary of the Nusantara Group, a conglomerate owned by Prabowo’s family) to operate in the area surveyed by Ridlatama. In 2010, Ridlatama’s license was revoked, effectively completing Nusantara’s take over of Churchill’s operations. Churchill appealed to the Supreme Court of Indonesia but lost the case. In 2012, Churchill filed a case against the government of Indonesia at the International Center for Settlement of Investment Disputes, demanding $2 billion in compensation. Indonesia argued that ICSID had no authority to arbitrate. In 2014 ICSID ruled that it had the authority and the case is still ongoing.

Troops under Prabowo’s command kidnapped and tortured at least nine democracy activists in the months before the May 1998 Riots. In one testimony, a former detainee told of being tortured for days in an unidentified location, allegedly a military camp where most of their time was spent blindfolded, while being forced to answer repeated questions, mainly concerning their political activities. The abuse included being punched, terrorised physically and mentally, and given electric shocks. Later, in 2009, two of the nine men were candidates for Gerinda, Prabowo’s political party, and another served as his media adviser. Prabowo was also suspected of organising the kidnappings of another 13 activists (all of whom remain “missing”) between February 1997 and May 1998.

Prabowo was the wealthiest presidential candidate in the 2009 election, with assets of Rp 1.5 trillion (about US$150 million) and US$7.5 million.

In November 2011, Prabowo announced his intention to run in the 2014 presidential elections. Surveys published by the Center for Policy Studies and Strategic Development (Puskaptis) and by the Indonesian Survey Institute published on 23 February 2012 gave him the lead – but observers and activists cast doubt on the polls.

In March 2012, Gerindra named Prabowo its 2014 presidential candidate. The party’s slogan was then changed to Gerindra Menang Prabowo Presiden (Gerindra Wins, Prabowo Becomes President). Prabowo said he would run an investment-friendly administration if he won and that Indonesia needed more energy exploration. Furthermore, he said he had been in close contact with labour unions and believed rising worker discontent could be managed with a wise national budget. He promised to use military-style efficiency to push through chronically delayed infrastructure projects, as well as to create jobs in the archipelago’s backwaters by improving agricultural productivity. Another pillar to Prabowo’s platform was that he was solidly secular, and his party planned to protect the rights of minority religious groups in the Muslim-majority country.

As a 2014 presidential candidate, Prabowo’s past came under renewed scrutiny, with many organisations calling for him to step down. A coalition, which consisted of Imparsial, Kontras, the Setara Institute, and the Human Rights Working Group (HRWG), combined under the Civil Society Coalition Against Forgetting, visited the National Commission on Human Rights (Komnas HAM) in Jakarta on 7 May 2014 to urge the commission to re-investigate Prabowo. A 27 June 2014 report indicated that an investigative journalist, Allan Nairn, had been threatened with arrest “for revealing the former general’s role in human rights abuses.”

In 2014, the regent of East Kutai, Isran Noor, publicly endorsed Prabowo as a presidential candidate. He also considered pressing criminal charges against Churchill, alleging that Churchill forged its license.

On 22 July 2014, the day that the KPU was due to announce its official tally, Prabowo withdrew from the race after having insisted on his victory since the initial quick counts were released, although the majority showed Jokowi ahead. He attributed this withdrawal to Indonesia “fail[ing] in its duty to democracy” because of “massive cheating that is structured and systematic”, and stated that he and Hatta “exercise our constitutional right to reject the presidential election and declare it unconstitutional”. His speech, aired live, implied he would challenge the results in the Constitutional Court. Later reports indicated confusion over whether Prabowo had resigned from the election or simply rejected the count.

Following the announcement, the value of the Indonesian rupiah dropped by 0.3%, and the JSX Composite fell by 0.9%. Observers denied Prabowo’s allegations of cheating, finding that the elections were “generally fair and free”; Maswadi Rauf of the University of Indonesia stated that there was “no sign of significant fraud”, and that Prabowo’s withdrawal simply reflected “the real attitudes of the elite, who are not yet ready to accept losing”. On 21 August 2014, the Indonesian Constitutional Court rejected his claim of fraud, confirming his election loss.

In November 2017 an investigation conducted by the International Consortium of Investigative Journalism cited his name in the list of politicians named in “Paradise Papers” allegations.

On 18 September 2017, at the launch of a book on his father’s political economy theory, Prabowo made a speech warning Indonesia could break apart in 2030. “In other countries, they have made studies, where the Republic of Indonesia has been declared no more in 2030,” he said. A video clip of the speech was posted to Gerindra’s official Facebook page on 18 March 2018. When asked which studies Prabowo was referring to, Gerindra official Elnino M. Husein Mohi said, “Prabowo has read various writings of people that are outside the country, intellectual observers that exist. You can also see them online.” It was subsequently revealed the “studies” were actually a 2015 science-fiction war novel called Ghost Fleet by American authors August Cole and P.W. Singer. A note by the authors at the start of the book states: “The following was inspired by real-world trends and technologies. But, ultimately, it is a work of fiction, not prediction.” Bemused by Prabowo citing the book, Singer posted on Twitter: “Indonesian opposition leader cites #GhostFleet in fiery campaign speeches… There have been many unexpected twists and turns from this book experience, but this may take the cake.”

On 12 April 2018, Prabowo announced he would contest Indonesia’s 2019 presidential election if he could obtain sufficient support from other political parties. Indonesian media had speculated on whether Prabowo would become a presidential candidate or a “king-maker” giving his support to another candidate. Prabowo’s brother Hashim in March 2018 said health and logistical factors had to be considered before the party announces a presidential candidate.

In April 2018, John McBeth reported Maritime Coordinating Minister Luhut Panjaitan had held a series of meetings with Prabowo, culminating in the proposal of a joint Widodo-Prabowo ticket for the 2019 election. Luhut reportedly lost his enthusiasm after Prabowo allegedly said he would want to be in charge of the military and seven seats in any new cabinet. Fadli Zon denied Luhut and Prabowo had discussed politics, claiming they merely spoke about Europe’s move to limit imports of Indonesian palm oil. Gerindra official Andre Rosiade also dismissed the report as a hoax.

On 10 August 2018, Prabowo registered at the KPU office for the 2019 presidential election with Sandiaga Uno as his running mate and with the support of Gerindra, PKS, PAN, the Democratic Party and Berkarya Party. The Democratic Party had wanted Prabowo to choose Agus Harimurti Yudhoyono as his running mate. Following the election, ‘quick counts’ conducted at polling stations by independent institutions authorised by the government indicated Widodo had won by a margin of about 10%, but Prabowo claimed victory, insisting a real count by his side showed he received 62% of the vote.

In late 2018, Prabowo was ridiculed after erroneously stating that Haiti, a republic in the Caribbean, is an African country. In a speech made on 23 December 2018 in Solo, Central Java, Prabowo said the Indonesian government had driven part of Indonesia’s wealth offshore. “If this continues to go on, Indonesia will continue to be impoverished,” he said. “We, Indonesians, are on par with African impoverished countries such as Rwanda, Haiti, and small islands like Kiribati, which we don’t even know where it’s located,” he added.

On 23 October 2019, Prabowo was inaugurated as Indonesia’s Minister of Defence by president Joko Widodo.

Following an incident in late 2019 where Chinese vessels violated Indonesian EEZ off the Natuna Islands, Prabowo called for a cautious response, referring to China as a “friendly nation”, for which he was criticised by netizens for being “too soft”. He also ordered the deployment of additional navy vessels in the region in response to the incident.

On 17 January 2019, in the first debate between the candidates in Indonesia’s April 2019 presidential election, Prabowo said some Indonesian governors deserve higher salaries considering the size of their provinces. He gave the example of Central Java province, which he claimed is larger than Malaysia (in population) . Local media reports pointed out that Central Java is 32,544.12 square kilometres, while Malaysia is 330,323 square kilometres. After the media reported on the error, Prabowo’s campaign team claimed he had actually been referring to the population totals of Malaysia and Central Java.

In October 2020, Prabowo visited the United States despite his previous ban from entering the country, in his capacity as Minister of Defense after being invited by his US counterpart Mark Esper and a visa was issued for him. Several human rights organisations, including Amnesty International, had previously called for the Trump administration to cancel the visit. Prior to this, Prabowo also visited China in December 2019.