The two dozen bodies were taken to hospitals in the Batken region in the southwest.
About 90 people were injured on the Kyrgyz side in the clashes.
The conflict between border guards of the two countries started early Friday.
Each side accused the other of violating agreements but they agreed to a cease-fire as of 4 p.m. local time (2200GMT).
The region is experiencing tension from a border dispute, including agricultural irrigation, animal grazing, smuggling and illegal border crossings.
Kyrgyzstan closed its customs gates with Tajikistan on May 21, 2021, until the border issue is resolved.
More about: Kyrgyzstan Tajikistan
