During the 2021 Kyrgyzstan–Tajikistan conflict, he led the Kyrgyz response to the clashes. On April 30, he held a telephone conversation with the President of Tajikistan Emomali Rahmon, during which he agrees to participate in a face-to-face meeting in Dushanbe in the second half of May. He also proposed the creation of a peacekeeping commission composed of elders from both countries. Later that day, Japarov addressed the Kyrgyz people, where he called for calm particularly from youth, underlining that the Tajik leadership don't want a war with Kyrgyzstan, noting their experience in the Tajik Civil War. At the same time, he also accused "certain forces" of destabilizing the situation on the border. He declared 1 and 2 May as a period of nationwide mourning.