A goal in time added-on robbed the Gills of a deserved point at the Coral Windows Stadium.
Steve Williams rose to head home the only goal of the game to extend the visitors woeful away record and complete a bad day for the Gills travelling supporters, many of whom had struggled to make the kick-off due to problems on the M1.
There certainly weren't too many on target attempts throughout the 90+ minutes, from either side, so it was gutting to lose to such a late goal.
The Gills were workman-like throughout and what makes things worse was the fact that City looked well beatable for long periods of the game.
This result saw Peter Taylor's side leap-frog the Gills who now find themselves 20th in the table.
There was just one enforced change in the starting XI, with Tony Sinclair missing through the back injury sustained against Shrewsbury last weekend, boss Andy Hessenthaler brought Josh Gowling back into the side.
The first threat on either goal came in the ninth minute. Robbie Threlfall curled in a deep free-kick from wide right, Lance Cronin failed to get anywhere near it and home skipper Shane Duff coming in behind headed wide of the open goal.
Moments later a cross from Luke O'Brien was headed over the top by City's beanpole striker Luke Oliver, who is normally more widely recognised as a central defender.
City had plenty of the possession early on but they really failed to threaten the Gillingham goal too often even with the visitors sitting a little too deep at times.
As the minutes ticked by the home fans became more and more frustrated as their struggling side failed to make a breakthrough.
The Gills first chance came in the 22nd minute, a long range strike from Danny Spiller wasn't taken cleanly by keeper Jon McLaughlin but he was able to collect the loose ball easily.
After starting with a 4-4-2 formation the Gills changed to 4-1-4-1as they tried to get a grip on the game. Jack Payne sat in front of the back four, Mark Bentley moved into the middle alongside Spiller, Cody McDonald moved to the right of midfield leaving Adebayo Akinfenwa to plough a lone furrow up front.
In a complete reversal of the early play, the tactical change certainly worked as the Gills began to get a lot of the ball, keeping possession well when they had it and pushed the Bantams deeper themselves.
McDonald then nicked the ball off a defender, strode forward before seeing his 20-yarder deflected wide.
Bentley chasing back created the next opening in the 42nd minute. He won the ball, Akinfenwa laid it off and Jack Payne fired over the top.
City boss Peter Taylor made two changes at the break bringing on former England international Lee Hendrie and Leon Osborne.
The second-half began with McDonald heading wide at one end and Osborne dragging a shot across the face of goal at the other.
For some reason this half began very heated with a number of niggling fouls which seemed to culminate with Osborne lucky to escape with just a yellow card for a challenge from behind on Barry Fuller. The one thing the tackles flying in did do was get the home crowd behind their team.
Hendrie, who earlier put a header over, had Bradford's first shot on target in the 61st minute but his bobbling effort failed to test Cronin.
The Gillingham boss made a double substitution in the 64th minute. Curtis Weston and Dennis Oli replacing Palmer and Akinfenwa as they went back to 4-4-2.
Stanley Aborah came on for his Gills debut in the 77th minute when he replaced McDonald. This brought another change of formation, the former Ajax midfielder sitting behind lone striker Oli.
The Gills had a great chance in the 82nd minute. Spiller put in free-kick from the left and Aborah, unmarked, headed straight at McLaughlin.
Two minutes later it was the home team that had a chance. Oliver played a ball through to Osborne but his low, right-foot shot went wide of the far post. Whether it took a deflection or Cronin got a touch it was hard to see but referee Ollie Langford awarded a corner.
Skipper Fuller got his name taken in the 89th minute for a challenge on Osborne near half-way.
Then in the three minutes of added time Bradford struck a winner. Following the award of a soft free-kick the Gills rearguard failed to clear properly and Tommy Doherty played in a high ball from the right . Steve Williams rather easily rose above Cronin to head home although the Gills keeper claimed he had been fouled. However it looked from afar that he had simply mis-timed his non-existent jump!
Gareth Evans still had time to drag another chance wide but by then the damage had been done.
It is now 16 months or 27 league games if you prefer, since the last away win at Rochdale. The next away trip is another long haul to play Accrington Stanley who are currently unbeaten.
Bradford City: McLaughlan, Duff, Oliver, O'Brien, Threlfall (Hendrie HT), Hunt, Bullock, Doherty, Williams, Moult (Evans 66), Speight (Osborne HT).
Unused Subs: Rehman, Daley, Saxton, Syers
Gillingham: Cronin, Fuller, Gowling, Lawrence, Nutter, Bentley, J Payne, Spiller, Palmer (Weston 64), McDonald (Aborah 77), Akinfenwa (Oli 64).
Unused Subs: Julian, Maher, McCammon, S Payne
Attendance: 10,722 (290 Gills)
Referee: Oliver Langford
Assistants: Ian Dudley and Darren Handley
Fourth Official: Duncan Street