Aaron Mclean gave the hosts a 10th-minute lead with his first goal for the club. Mclean, who had gone 10 matches without scoring since joining the Bantams from Hull in January, scored with a half volley from just inside the six -yard area after the Gills failed to deal with left-back Adam Drury's cross.
The goal was a reward for Bradford's bright start and they dominated the first half without being able to add a second goal.
Gillingham were a more lively team after the break and, after making a double substitution at the interval, equalised after 57 minutes.
Substitute Adebayo Akinfenwa played a pass behind the Bradford defence and Cody McDonald beat the on-rushing Jon McLaughlin to the ball before turning it past the goalkeeper.