Slovenia's most popular politician, Drnovšek began his political career in the late 1980s. He was elected as the Slovene representative in the collective presidency of the former Yugoslavia in the April 1989 elections. He was head of the presidency of the former Yugoslavia from May 1989 to May 1990, and during Slovenia's independence negotiations, he served as the principal negotiator between the Slovene leadership, the leaders of the former Yugoslavia, and the Yugoslav army. He negotiated the withdrawal of the Yugoslav army from Slovenia in July 1991.
Drnovšek became the head of the Liberal Democratic Party of Slovenia in March 1992, and in April, was elected prime minister by the National Assembly. He was elected to that position four times. On 1 December 2002, he beat Barbara Brezigar, with 56% of the votes to 44%, to become Slovenia's second president.