Austin Grammer scored from 19 yards out on Middle Tennessee's opening drive, capping a 10-play, 75-yard effort. The Blue Raiders (6-5, 4-2 Conference USA) scored TDs on each of their first four possessions, totaling 294 yards in the process.
Stockstill, a redshirt freshman, was 27 of 38 and notched his seventh game with at least 300 passing yards of the season, including four in a row.
DaMarcus Smith's 1-yard run put North Texas (1-10, 1-6) on the board midway through the second quarter. But a TD pass from Stockstill and field goal put the Blue Raiders up by 24 at the half.
Middle Tennessee converted 10 of 15 third downs.
The loss gives North Texas only its second season with double-digit losses in the program's 91-year history.