In 1993, Amir began studying at Bar-Ilan University as part of its kollel program, mixing religious and secular studies. Amir studied law and computer science, as well as Jewish law at the Institute for Advanced Torah Studies. Amir was strongly opposed to the Oslo Accords. He participated in protest rallies against the accords on campus, was active in organising weekend bus outings to support Israeli settlers, and helped found an illegal settlement outpost. He was especially active in Hebron, where he led marches through the streets.

In 1994, during his university studies, Amir met – and began a (non-sexual) relationship with – Nava Holtzman, a law student from an Orthodox Ashkenazi family. In January 1995, after five months, Holtzman ended the relationship after her parents objected due to Amir’s Mizrahi background. She married one of his friends soon afterwards. Amir, who attended the wedding, went into a deep depression.

On November 4, 1995, after a demonstration in Tel Aviv’s Kings of Israel Square (now Rabin Square) in support of the Oslo Accords, Amir waited for Rabin in a parking lot adjacent to the square, close to Rabin’s official limousine. There, he shot Rabin twice with a Beretta 84F .380 ACP calibre semi-automatic pistol, and injured Yoram Rubin, a security guard, with a third shot. Amir was immediately seized by Rabin’s bodyguards. Rabin was rushed to Tel Aviv Sourasky Medical Center where he died on an operating table 40 minutes later of blood loss and a punctured lung. According to the court, Yigal Amir’s brother Hagai and his friend Dror Adani were his accomplices in the assassination plan.

On December 19, 2001, the Knesset by majority of 62 members approved the Yigal Amir Law, which prohibits a parole board from recommending pardon or shortening time in prison for a murderer of a Prime Minister. In the discussion that ensued, it was hoped the law would prevent another political murder.

Amir was held in solitary confinement in Beersheba’s Eshel Prison, and moved in 2003 to the Ayalon Prison in Ramla, where a solitary confinement wing was built especially for him. In 2006, he was transferred to Rimonim Prison in Tel Mond, near Netanya. He was also granted the privileges of having no surveillance cameras in his cell, the right to receive visitors in the visiting room, rather than in his cell, and the right to speak with other prisoners. Amir was interviewed by the Israeli press in 2008, but the planned broadcast was controversial, and subsequently cancelled. As punishment for giving the interview, Amir was moved to Ramon Prison, and had a number of privileges withdrawn, including the removal of his TV and DVD player and the refusal of family visits; Amir went on a hunger strike in protest. In February 2010, the Nazareth District Court permitted the Ynet internet news service to interview Amir.

Amir is married to Larisa Trembovler, who was born in Russia. She has a Ph.D. in philosophy. She has published a novel in Russian (A Mirror for a Prince), and is an Orthodox Jew. She met Amir in Latvia, where he was teaching Judaism. After her immigration to Israel, she visited Amir with her then-husband, Benjamin (with whom she has four children), for humanitarian reasons. She expressed ideological support for Amir, and they began to correspond and speak on the phone. She divorced Benjamin in 2003.

Trembovler announced that she was engaged to Amir and wanted to marry him, while he was in jail. In January 2004, after their request was filed, the Israel Prisons Service declared it would not permit the marriage. In April 2004, the matter was brought before the Tel Aviv District Court. At the time, the Prisons Commissioner instructed his legal aides to defend the decision based on security considerations. But Amir’s lawyers said this claim violated their client’s basic rights and would not hold up in court. They noted that several Palestinians serving multiple life terms for crimes such as murder have been permitted to marry in prison. Legal analysts have said the Supreme Court would likely uphold any appeal by Amir’s lawyer, unless specific legislation is enacted prohibiting him from marrying. In August 2004, Trembovler and Amir were wed in a surreptitious proxy marriage. Under Jewish law, a prospective husband can grant a form of “power of attorney” to a chosen representative, who can then transfer a wedding ring, or something of similar value, to the prospective wife. In July 2005, their marriage was validated by an Israeli rabbinical court. Trembovler submitted a petition after the Interior Ministry refused to register her and Amir as a married couple. Israel’s Justice Ministry defined Amir’s marriage as “problematic” because according to a past ruling, a marriage ceremony not conducted in the presence of a rabbi from the Chief Rabbinate is unrecognised.

On February 6, 2006, Haaretz reported that Attorney General Menachem Mazuz had ordered the Interior Ministry to register Amir and Trembovler as a married couple. They then filed requests with the Prison Authority and petitions to court to enable them to hold conjugal visits or conceive a child through artificial insemination.

In March 2006, the Israeli Prison Service approved Amir’s petition for in vitro fertilisation. The service was to study how this process would be conducted without Amir leaving the prison. A week later, Amir was caught handing a pre-prepared bag of semen to his wife, and the visit was terminated. After the incident, a disciplinary tribunal barred visits from his wife for 30 days, and phone calls for 14 days. He was fined NIS 100 (then US$21). When the IVF treatments were withheld due to a petition by several members of Knesset, Amir went on hunger strike. After being warned that hunger strikes are in violation of prison regulations, some of his privileges were cancelled.

From time to time, radical Israeli right-wing organisations carry out campaigns (via posters or videos) which call for the release of Yigal Amir. Such a campaign was held in October 2007 in which the prominent Israeli singer Ariel Zilber also participated. In response to this campaign, the Israeli Internal Security Minister Avi Dichter stated: “This man is in the closest status a person can be to a death sentence”, and also added that, “A reduction of his sentence is impossible and illogical, and it will surely accompany him until he would pass away”. His brother Hagai was released from prison on May 4, 2012.

Up until October 20, 2006, the Shin Bet security service had opposed unsupervised visits. Four days later, Amir was allowed a 10-hour-long conjugal visit. Five months later, it was reported that Trembovler was pregnant. On October 28, 2007, she gave birth to a son, who was named Yinon Eliya Shalom. The brit milah was held in prison on November 4, 2007, the 12th anniversary of Rabin’s assassination.

In July 2010, after 15 years of solitary confinement, Amir appealed to the Petah Tikva District Court to be permitted to participate in group prayers in accordance with Jewish law. He claimed that the terms of his imprisonment were worse than any other prisoner in the history of the State of Israel, on the grounds that no other prisoner had been in solitary for this amount of time. He said that failure to allow him to pray in synagogue would be a violation of his right to freedom of worship. In August 2010, the court ruled that Amir would be allowed to meet another prisoner for prayer three times a week, and that he would be allowed to study Torah with another prisoner once every two weeks.

In July 2012, it was announced that Amir would be released from solitary confinement. Under his new prison conditions, he will be allowed to watch television and use a phone more frequently. Though he will not be moved to an open cell block, where prisoners are allowed to spend most of the day outside their cells, he will be allowed to meet other prisoners during his two hours’ exercise in the prison yard.

On July 8, 2015, a documentary on Yigal Amir, Beyond the Fear, was premiered in Jerusalem. The film explored the thorny drama of the Moscow-born intellectual Larisa Trembovler, who married assassin Yigal Amir after he was sentenced to life in prison and, following a court battle for a conjugal visit, gave birth to their son in 2007. The late filmmaker Herz Frank, who died in 2013, spent about 10 years following Trembovler, receiving unprecedented access to her and their son, Yinon. Rabin’s granddaughter called the film a “cynical use of the freedom of expression with intent to harm it”.

The 2019 film Incitement consists of a portrayal of the factors that led Amir to commit the assassination. It won the 2019 Ophir Award.

In 2020, Amir requested a furlough from prison to attend his son’s Bar Mitzvah, which the Israel Prison Service denied. Amir appealed the decision to the Beersheba District Court, which upheld the refusal.