In 1976, Akayev returned to Kyrgyzstan to work as a scientist and teacher in the field of quantum optics. In 1986, he was summoned to Moscow to serve in the Soviet Central Committee Department on Science and Education. He was elected vice president of the Kyrgyz Academy of Sciences in 1987 and in 1989 became its president. In 1989, he was elected by the constituents of the Naukatsk district to the newly created USSR Congress of People's Deputies and subsequently selected to serve in the Soviet of Nationalities of the USSR Supreme Soviet, where he was a member of the Constitutional Oversight Commission and the committee on economic reform. As a legislator, he traveled extensively, meeting with constituents. As a result, he came to the conclusion that he would shift his career from science to politics in order to contribute to the betterment of Kyrgyzstan. In a significant speech at the Congress of People's Deputies in December 1989, he called for marketization to improve the Soviet economy.
In the summer of 1990, ethnic tensions in the Osh region led to mass demonstrations in Bishkek against Communist Party rule, with demands for the ouster of the Communist Party leader Masaliyev. When the Kyrgyz Supreme Soviet convened in October 1990, deputies aligned in a democratic bloc narrowly defeated Masaliyev's bid to become president.
Akayev's supporters urged him to quickly return to Kyrgyzstan from his legislative duties in Moscow, and after repeated voting, elected him to the newly created post. In an uncontested direct popular election held in October 1991, he was reelected president, winning 95% of the vote.
In the face of growing legislative and regional opposition to his rule, Akayev held a popular referendum in January 1994 on whether he should finish out his term, winning support from 96.2% of the voters to continue his reforms. In September 1995, Akayev's supporters submitted a petition signed by 1.2 million (52% of the voting-age population) urging the legislature to approve a referendum extending Akayev's term to the year 2001. After contentious debate, the legislature rejected holding a referendum, and Akayev instead announced that a presidential election would be held on 24 December 1995. Thirteen candidates were registered, but 10 were disqualified, leaving Akayev, Masaliyev, and former Speaker of Parliament Medetken Sherimkulov. Akayev won reelection to a five-year term, receiving 72% of the vote in a race deemed generally "free and fair" by international observers, though questions were raised about the disqualifications. In July 1998, Akayev hailed a Constitutional Court decision permitting him to run for a third term in the year 2000. He won that election with 74.4% of the vote. However, election monitors from the Organization for Security and Cooperation in Europe (OSCE) who observed the voting concluded that it was not "free and fair," pointing to problems such as the disqualification of prominent opposition parties and candidates, the progovernment composition of electoral boards, government harassment of opposition candidates, and irregularities in vote-counting. Akayev rejected these assessments as overlooking Kyrgyzstan's democratic and economic accomplishments. Among the problems, opposition Dignity Party head Feliks Kulov received more votes than his opponents in the first round of the February 2000 legislative race, but was heavily defeated in the second round through apparent legerdemain, according to the OSCE. Kulov was later arrested and accused of crimes that had been committed several years earlier.