Jeenbekov resigned from the post of Prime Minister on 21 August 2017, after being named as an official candidate in the 2017 presidential election. He stated that he "wanted to be in an equal position with other presidential candidates."
The election was held on 15 October 2017. Kyrgyzstan's central election commission reported a total of almost 1.7 million votes cast, of which Jeenbekov won 54.74 percent. Jeenbekov's election marks the first democratic transfer of power in a Kyrgyz election. Azay Guliyev confirmed the election to be one of the few peaceful elections in Kyrgyzstan's history.
Jeenbekov opened the Central Mosque of Imam Sarakhsi, which is the largest mosque in Central Asia, with his Turkish counterpart Recep Tayyip Erdoğan during his visit to Bishkek in early September of 2018. During his visit, Erdoğan pressured Jeenbekov to take the appropriate measures to deal with Turkish Islamist leader Fethullah Gülen.
Jeenbekov Received the Hungarian Prime Minister Viktor Orbán at the Cholpon-Ata State Residence the next day of the opening of The 2018 World Nomad Games, Jeenbekov thanked the prime minister for becoming the first Hungarian leader to visit the country since it's independence.