Joya was born on April 25, 1978, in the Farah Province, in western Afghanistan. Her father was a former medical student who lost a leg while fighting in the Soviet–Afghan War. In 1982, when she was 4 years old, her family fled Afghanistan to live as refugees in neighboring Iran. She got involved in humanitarian work while in eighth grade.

After the Soviet withdrawal, Joya returned to Afghanistan in 1998 during the Taliban’s reign. As a young woman she worked as a social activist and was named a director of the non-governmental group, Organisation of Promoting Afghan Women’s Capabilities (OPAWC) in the western provinces of Herat and Farah. She is married, but has not revealed the name of her husband due to fear for his safety.

Malalai Joya gained international attention when, as an elected delegate to the Loya Jirga convened to ratify the Constitution of Afghanistan, she spoke out publicly against the domination of warlords on December 17, 2003.

Joya was elected to the 249-seat National Assembly, or Wolesi Jirga in September 2005, as a representative of Farah Province, winning the second highest number of votes in the province, with 7.3 percent of the vote. At an impromptu news conference after the swearing-in ceremony in December 2005, she offered her “condolences” to the people of Afghanistan “for the presence of warlords, drug lords and criminals” in the Parliament. “The people of Afghanistan have recently escaped the Taliban cage but still they are trapped in the cage of those who are called warlords”

In 2006, the Washington Post said of Joya: “Her truth is that warlords should not be permitted to hide behind ‘the mask of democracy to hold on to their chairs’ and their pernicious pursuits at the expense of poor, ‘barefoot’ Afghans who remain voiceless and disillusioned. The warlords are corrupt ‘war criminals’ who should be tried, and incorrigible ‘drug dealers’ who brought the country to its knees, she said.”

Malalai Joya appeared at the Federal Convention of Canada’s New Democratic Party (NDP) in Quebec City on September 10, 2006, supporting party leader Jack Layton and the NDP’s criticism of the NATO-led mission in southern Afghanistan. She said, “No nation can donate liberation to another nation.”

On May 7, 2006, Malalai Joya was physically and verbally attacked by fellow members of parliament after accusing several colleagues of being “warlords” and unfit for service in the new Afghan government. “I said there are two kinds of mujahedeen in Afghanistan,” Joya told the Associated Press. “One kind fought for independence, which I respect, but the other kind destroyed the country and killed 60,000 people.” In response, angered lawmakers shouted death threats and threw empty plastic water bottles at Joya, who was shielded by sympathetic colleagues.

Malalai was in Sydney, Australia, on March 8, 2007, as a guest of UNIFEM, speaking about women’s rights in Afghanistan in honor of International Women’s Day.

Malalai returned to Canada in November 2007 and addressed 400 people at the Steelworkers Hall on Cecil Street in Toronto. She then addressed a small group of union activists and activists at the Ontario Federation of Labour.

On May 21, 2007, fellow members of the Wolesi Jirga voted to suspend Malalai Joya for three years from the legislature, citing that she had broken Article 70 of the Parliament, which had banned Wolesi Jirga members from openly criticizing each other. Joya had compared the Wolesi Jirga to a “stable or zoo” on a recent TV interview, and later called other members of parliament “criminals” and “drug smugglers.” She is reported to have referred to the House as “worse than a stable”, since “(a) stable is better, for there you have a donkey that carries a load and a cow that provides the milk.”

On June 21, 2007, one month after Joya was suspended, Joya supporters in Melbourne staged protests to the Afghan government to reinstate Joya to the parliament. In November 2007, an international letter was launched with a number of prominent signatories supporting the call for her reinstatement to parliament.

In November 2008 Malalai visited the Norway Social Forum, and spoke before the 1900 participants. She also participated in a debate with the Norwegian Foreign Minister, and asked Norway to pull its troops out of Afghanistan.

In December 2008, Malalai Joya was invited by Amnesty International India to New Delhi for the International Week of Justice Festival, December 5–10, 2008, commemorating the 60th anniversary of the Universal Declaration of Human Rights. Joya participated in two public forums for the festival at Jamia Millia Islamia and Alliance Francaise on the issues related to post-war Afghanistan, female empowerment and torture.

In January 2008, after her suspension, Joya spoke to Rachel Shields and said that the government was not democratically elected and they were “trying to use the country’s Islamic law as a tool with which to limit women’s rights.”

On April 18, 2008, the Governing Council of the Inter-Parliamentary Union, unanimously adopted a resolution at its 182nd session in Cape Town in favour of Malalai Joya which “Calls on the authorities at the same time to do everything in their power to identify and bring to justice those making the death threats against Ms. Joya.”

On October 7, 2008, six women Nobel Peace Prize laureates (Shirin Ebadi, Jody Williams, Wangari Maathai, Rigoberta Menchú, Betty Williams and Mairead Maguire) in a joint statement supported Malalai Joya: “We commend this courage, and call for Joya’s reinstatement to Afghanistan’s national parliament… Like our sister Aung San Suu Kyi, Joya is a model for women everywhere seeking to make the world more just.”

In October–November 2009 Joya was on book tour to the US and Canada and addressed many anti-war rallies and gatherings. She called for withdrawal of all troops from Afghanistan.

On November 24, 2009, New Statesman (UK) ranked Malalai Joya in the sixth place on its list of “The 50 people who matter today… for good and ill”, calling her “Afghanistan’s answer to Aung San Suu Kyi.”

During her suspension, Malalai Joya stayed active by giving interviews to western journalists and by writing articles for western newspapers on her views on the situation of Afghanistan. In 2009 she made a tour through the United States and Canada to advocate her cause and to promote her book.

Joya has written a memoir with Canadian writer Derrick O’Keefe. The US and Canadian version of the book was published in October 2009 by Scribner under the title of A Woman Among Warlords: The Extraordinary Story of an Afghan Who Dared to Raise Her Voice in 224 pages. The Australian and British versions have already been published by Pan Macmillan and Rider under the title of Raising My Voice: The Extraordinary Story of an Afghan Who Dares to Speak Out. It has so far been published in German titled Ich erhebe meine Stimme – Eine Frau kämpft gegen den Krieg in Afghanistan, in Norwegian under the title Kvinne blant krigsherrer – Afghanistans modigste stemme and in Dutch under the title Een vrouw tussen krijgsheren and in Japanese under the title Together with Afghan People.

In February 2010, at the event of the presentation in Paris of “Au nom de mon peuple”, the French publication of her memoir “A Woman Among Warlords”, Joya expressed her wish to make a political comeback in the Afghan parliamentary elections scheduled for September. Allegedly, supporters in five Afghan provinces asked her to represent them. These included Nangarhar, Nimroz, Takhar, Kabul and also Farah — the western province that sent her first to the loya jirga that ratified the Constitution, then elected her to Parliament in 2005. Preparing for her comeback, she said she would prefer for security reasons to run as a candidate in the capital. However, at the occasion of the marriage of one of her body guards in July 2010, she revoked her earlier announcement to participate in the parliamentary elections.

Because she is “unemployed” and “lives underground”, the United States denied Joya a travel visa in March 2011 which sparked a public campaign by her supporters to pressure the US government. She was scheduled to speak at several different places in the United States, including Pace University in Manhattan and St. Mary’s College of Maryland. Joya stated that “[the Afghan government] has probably requested the U.S. to not let me enter … because I am exposing the wrong policies of the U.S. and its puppet regime at the international level.” However, the U.S. State Department later explained that a visa has been issued to Joya.

Joya started her US speaking tour on March 25, 2011 from Boston where, along with Professor Noam Chomsky, she gave a presentation on the Afghan war to 1200 people at Harvard’s Memorial Church.

On March 21, 2013 Joya addressed a big Nowruz festival in Khewa district of Nengrahar province in South of Afghanistan. Around 5000 people gathered in this event to celebrate Afghanistan’s New Year (1392).

On March 24, 2013 Joya joined the support network in defense of Chelsea Manning. She published a photo holding a sign which read “I am Bradley Manning!” She called her “great anti-war soldiers, who represent the shining face of America.”

In 2016, Joya criticized peace talks which saw Gulbuddin Hekmatyar, a long-time Islamist insurgent leader, and his militants pardoned in return for them ending hostilities with the Afghan government. She claimed the agreement “signals more horror and bloodshed” and said that Gulbuddin was a “devious rascal”.

In 2017, she stated that things had become worse for activists since the fall of the Taliban regime, claiming “Under the Taliban, we had only one enemy – now we have Taliban, warlords, Islamic State, occupation forces that keep dropping bombs, and the so-called technocrats, who have compromised in exchange for money and power.”