In-form attacker Dominic Poleon made it two goals in two consecutive games to help secure back-to-back wins for the Bantams at the start of the new league season.
Poleon pounced in the nineteenth minute at the MEMS Priestfield Stadium to convert Alex Jones' pull back and help claim City's maiden away victory of the campaign at the first attempt.
Poleon's afternoon could have got even better on the stroke of half time but the attacker fired wide after rounding Gills 'keeper Tomas Holy.
Gillingham were reduced to ten men for the final fifteen minutes when Conor Wilkinson was given a straight red for a lunge on Timothee Dieng.
Despite their numercial disadvantage though, Gillingham thought they had snatched a late equaliser in the final minute of injury time but Tom Eaves' close range strike was ruled out for offside.
City, wearing their white and claret 'third' shirts for the first time, started the game in confident fashion but Gillingham were an early threat from long throws.
One such delivery from Mark Byrne in the fifth minute was headed on into the six yard box by Wilkinson but an alert Matthew Kilgallon was on hand to hook clear.
City still looked the more likely scorers in the opening stages though, and Dieng was denied by Holy after the French midfielder had worked a good shooting opportunity deep inside the box.
Gills defender Alex Lacey then had to be alert soon after to kick clear after Poleon had beaten Luke O'Neill out wide and played into the middle.
Just a minute or so after the chance, Poleon was involved again as the former AFC Wimbledon forward fired City into the lead.
Good work on the right from Jones saw the attacker cut the ball back to Poleon and his fellow forward was on hand to help it into the far bottom corner with a side-foot finish.
Gillingham looked to respond soon after but Mark Byrne fired over from outside the box and Lacey headed over on the stretch from Lee Martin's far post corner.
Jake Reeves, one of four City players booked on the day, dusted off his shooting boots just after the half hour mark, the all-action midfielder firing narrowly over from just outside the box after Tony McMahon had fed the ball into his path direct from a corner.
Colin Doyle was forced into his first meaningful save of the afternoon ten minutes from the break when City failed to clear another Byrne long throw-in into the area.
The ball eventually dropped into the path of Josh Parker but his effort from a tight angle over by the far post was repelled by City's Irish shot-stopper.
An encouraging opening period for the Bantams could have got even better just before the break when Poleon dispossessed Ehmer to give him a clear run on goal.
Poleon confidently rounded Holy in the Gills goal but his left-footed effort was scuffed wide with the goal open.
There was still time in the half for Gillingham to engineer one more opening but Lacey headed over from a decent position in the middle following Martin's inviting free-kick delivery into the six-yard box.
Attacking to their main Rainham End Stand after the break, Gillingham seemed to step up their efforts to get themselves back into the game.
Parker squandered a promising chance for the hosts just past the hour when O'Neill's clipped cross fell nicely into his path.
The striker seemed in a good position in the middle to convert but he poked wide of the post.
To kick-start City's attacking efforts after the restart, Bantams boss Stuart McCall introduced Alex Gilliead and Paul Taylor from the bench within eight minutes of each other in the second period.
Following Parker's earlier opening, Josh Wright missed the target himself with a free header after he was found unmarked in the middle from Martin's corner.
Just as Gillingham looked as they might be building up a head of steam though, their prospects in the game were dealt a blow when Wilkinson was given his marching orders for a stretching challenge on Dieng by the corner flag.
Wilkinson's dismissal clearly boosted City's chances of seeing out the game, and McCall's men proceeded to take control of the football in the game's closing stages.
Nicky Law, Poleon and Taylor all saw efforts saved by Holy as the Bantams tried to wrap up the three points with a second goal.
Those missed opportunities looked like they might end up cruelly denying City the victory after late drama in the final seconds of injury time.
From a Martin free-kick delivery from wide into the box, Scott Wagstaff kept the ball alive with a low drive and Eaves was on hand to convert from close range.
Any home celebrations were short-lived, however, as the linesman's flag was up straight away to rule out the goal.