Gary Jones scored direct from a corner as Bradford extended Gillingham's winless run to eight League One games.
Jones put the Bantams in front when his corner squeezed in at the front post.
James Hanson almost made it 2-0 to the visitors but his close-range header went wide.
Cody McDonald squandered Gillingham's best chance in the second-half as he blazed his shot over the crossbar from four yards out as they slumped to the bottom of the table.
VIEW FROM THE DRESSING ROOM
Gillingham manager Martin Allen:
"It was a disappointing performance, I made two changes from an excellent performance at Coventry and I think I got it wrong.
"We were very poor first half, I've sat here from day one and backed players, but today there far too many players well below par.
"I've got to make some changes, it's been far too many games, the paying public deserve better than that.
"Some people are transfer listed, or for loans. We've had no enquiries for anybody."