1999–2000 Bosnia and Herzegovina Football Cup was the sixth season of Bosnia and Herzegovina's annual football cup.
The Cup was won by Željezničar who were first in the final group.
In the final stage of the competition, four clubs from the Football Federation of Bosnia and Herzegovina and the two clubs from the Football Federation of Herzeg-Bosnia joined the competition.
After a preliminary round, the remaining three advanced to the final group with only forward matches at the end of which the first-placed in the group won the trophy and qualified for the 2000–01 UEFA Cup (qualifying round).
The matches were played on 27 November 1999.