Isakov began his political career as a member of the town council of Osh as a member of the Social Democratic Party of Kyrgyzstan. He became Minister of Education and Science on 11 September 2019 following the resignation of Gulmira Kudaiberdiyeva. During his tenure, he introduced a program which sought to produce better quality textbooks in the Kyrgyz language. During the 2020 Kyrgyzstani protests, Prime Minister Kubatbek Boronov's cabinet was sacked. Although it was initially announced that ministers would remain in place, the Japarov administration formed a completely different staff. Almazbek Beichenaliev replaced Isakov.