Two of the six new planes made the first training flight in the morning, spokesman Michal Prejzek of the Caslav tactical air base said.
The Czech Republic will pay 19.6 billion koruna (654 million euros, 785 million dollars) for the lease of 14 Gripens for 10 years.
Its army will receive another eight planes from the Swedish manufacturer in August and later this year.
The MiG-21s had stopped complying with the needs of the Czech Republic within NATO, which it joined in 1999.
Prejzek said that two Gripens would always be alternately on 24-hour alert on the airfield or in training flights in the air.