On the morning of 31 October 1984, his mother was assassinated by her Sikh bodyguards to avenge Operation Blue Star; later that day, Rajiv Gandhi was appointed Prime Minister. His leadership was put to the test over the next few days as organised mobs rioted against the Sikh community, resulting in the death of thousands in Delhi alone. Nevertheless, that December, a nationwide sympathy vote for Rajiv's Congress party helped it win the greatest Lok Sabha majority (411 seats out of 542) in history.

Rajiv Gandhi was also mired in many controversies: the 1984 anti-Sikh riots, Bhopal disaster and Shah Bano case. In 1988, Gandhi reversed the coup in Maldives antagonising militant Tamil groups such as PLOTE. He was also responsible for first intervening and then sending Indian Peace Keeping Force troops for peace efforts in Sri Lanka in 1987, which soon ended in open conflict with the Liberation Tigers of Tamil Eelam (LTTE). In mid-1987, the Bofors scandal damaged his honest, corruption-free image and resulted in a major defeat for his party in the 1989 elections.

Rajiv Gandhi remained Congress President until the elections in 1991. While campaigning for the elections, he was assassinated by a suicide bomber from the LTTE. His widow Sonia became the president of Congress party in 1998, and led the party to victory in the 2004 and 2009 parliament elections. His son Rahul is a Member of Parliament and Vice President of the Congress. Rajiv Gandhi was posthumously awarded the highest civilian award by the government of India, Bharat Ratna in 1991.