Defence sources said the pilot spotted fire during the take off roll, aborted the take off and ejected safely.
The aircraft hit the barrier on the runway, sources said, adding that a court of inquiry has been ordered into the accident.
The aircraft was to take off for a routine sortie.
On Saturday, another MiG-21 trainer aircraft crashed in Rajasthan's Barmer district but no loss of life was reported with both the pilots ejecting safely.
Ambala Deputy Commissioner Prabhjot Singh, quoting a senior IAF official, said the incident occurred at around 8 pm. "The pilot is safe and has been taken to Army hospital for a check-up," Singh said.