Yigal Amir was born in Herzliya to an Israeli Orthodox Yemenite Jewish family, one of eight children. His father Shlomo was a sofer who held a post supervising the kosher slaughtering of chickens and taught Shabbat lessons at a local synagogue. His mother Geula was a kindergarten teacher, and ran a nursery school in family home's backyard. Amir attended a Haredi elementary school in Herzliya, and a high school yeshiva in Tel Aviv. He did his military service in the Israel Defense Forces as a Hesder student, combining army service in a religious platoon of the Golani Brigade with religious study at Yeshivat Kerem B'Yavneh. Despite being in a religious unit, even his comrades considered him a religious fanatic.
Following his military service, Amir was nominated by the religious-Zionist youth movement Bnei Akiva to teach Judaism in Riga, Latvia, as part of Nativ.
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 heavily opposed to the Oslo Accords. He participated in protest rallies against the accords on campus, was active in organizing 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.
During his years as an activist, Amir became friendly with Avishai Raviv, to whom he revealed his plan to kill Rabin. While Raviv posed as a right-wing radical, he was working for Shin Bet, the Israeli internal security service. Some rightists have accused the Shin Bet of having orchestrated the assassination to discredit them.
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.