Army spokesman Lt Gen Asim Saleem Bajwa said the aircraft was on a training mission when it crashed in Gujranwala district in Punjab.
"Both the crew members, instructor pilot Major Azhar and trainee pilot Captain Ahmed lost their lives in the crash," Bajwa said.
The immediate cause of crash was not known. The crash is the latest deadly accident to hit Pakistan's military.
(Reopens FGN 26)
District Police Officer Rai Zameer said the army's Mustaq jet crashed near Chenab Bridge, some 100 kms from Lahore.
The rescue teams reached the spot and shifted the bodies to the Combined Military Hospital Gujranwala district of Punjab.