The Bantams suffered a setback in their bid for the play-offs with defeat in Kent.
Phil Parkinson’s City remain ninth, seven points adrift of the top six in League One with four games to play.
John Marquis scored the only goal 18 minutes from time to eanr Gillingham the points.
Parkinson said: “We’ve had so many great moments to kill game.
“But when you don’t take those chances you’re always vulnerable to be punished.”