Both sides had accused each other of provocation and opening fire following a row over border demarcation.
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Tajikistan and Kyrgyzstan have signed a protocol to establish peace after a series of violent military clashes on the border left at least 100 people dead.
The documents were signed Tuesday by senior representatives from the two Central Asian countries.
"I really hope that today's signed protocol of mutual understanding, which we started at our commission with the respected Saimumin Satarovich, will bring peace to our countries. I am sure that peace is always better, peace will persist and we will always strive for this peace," said Kamchybek Tashiev, president of Kyrgyzstan's National Security Committee.
His Tajik counterpartpart Saimumin Satarovich said "real peace will come to our borders," describing the two countries as "brother nations."
Skirmishes started on the Kyrgyz-Tajik border on 14 September, and both sides accused the other of provocation and opening fire.
The conflict followed a row over border demarcation.
Authorities of Kyrgyzstan reported at least 59 fatalities from shelling and fighting while in Tajikistan, officials said 41 people were killed and dozens more wounded.