In an announcement published on the presidential website on Friday, Jeenbekov said, he does not want to go down in the history of Kyrgyzstan as a president who allowed bloodshed and shooting on its people. He has taken the decision to resign, he added.
He also called on newly-appointed Prime Minister Sadyr Japarov and other opposition politicians to take their supporters away from the capital so that peace could return to Bishkek.
On Wednesday Jeenbekov gave his approval to the new PM’s appointment after parliament voted for him a second time.
Kyrgyzstan has been in crisis since parliamentary elections on 4 October. Subsequent protests forced electoral officials to annul the results, and also toppled the government.