The countries' respective national security committee chiefs announced the agreement in a joint briefing on Saturday in Kyrgyzstan.
Two sides agreed to form working groups to help enforce the ceasefire, according to Kyrgyzstan's national security committee.
The groups would begin work at 0200 GMT on Sunday.
The Kyrgyz-Tajik border conflict can be traced back to opposing territorial claims in the border area of the two states.
The unclear demarcation of boundaries is regularly the trigger for partly armed clashes between Kyrgyz and Tajiks in the disputed areas.