The 1999–2000 Czech Cup was the seventh season of the annual football knock-out tournament of the Czech Republic. Winners Slovan Liberec qualified for the 2000–01 UEFA Cup.
44 teams took part in the preliminary round.
74 teams entered the competition at this stage. Along with the 22 winners from the preliminary round, these teams played 48 matches to qualify for the second round.
Čelákovice were the only team from the fourth level to take part in round 4.
The quarterfinals were played on 12 April 2000.
The semifinals were played on 2 and 3 May 2000.