Kane Vincent-Young’s first ever Town goal has given the Blues a 1-0 half-time lead at Gillingham.
Town boss Paul Lambert made four changes from the team which beat the MK Dons 1-0 on Tuesday but with the side again starting in a 3-5-2 system.
Ahead of keeper Tomas Holy, who was facing his old club, Luke Woolfenden returned on the right of the back three with skipper Luke Chambers and James Wilson.
Gwion Edwards was at left wing-back, a role he previously played at Peterborough and in the Leasing.com Trophy tie with Tottenham’s U21s, with Vincent-Young on the opposite flank.
Andre Dozzell came into the centre of midfield ahead of Cole Skuse and Flynn Downes, while Alan Judge was also back in the side playing in a free role off main striker Kayden Jackson.
James Norwood, who aggravated a long-standing groin injury on Tuesday dropped to the bench along with Jon Nolan, Emyr Huws and Luke Garbutt, who all started at Stadium MK after injury absences.
Gillingham’s starting XI included Stuart O’Keefe, who began his career as an academy scholar with the Blues, while ex-loanee Ben Pringle was on the bench.
After Town had seen most of the ball in the opening moments, the Gills struck the game’s first shot in the fourth minute, however, Olly Lee’s strike flew well over.
On the touchline, the two management teams had already exchanged words with Gillingham manager Steve Evans having begun a lively dialogue with the fourth official only seconds after kick-off following the award of a Blues freekick.
Town, with more than 2,500 fans watching them from the Brian Moore Stand, twice broke forward early on, despite starting scruffily. First Jackson was sent away down the right but was unable to find anyone with a low cross, then Downes fed Judge, whose cross found Jackson, but the striker was unable to find a team-mate with his knockdown.
On 14 the Blues carved out an opening with their best football up to that point. Dozzell, who had seen little of the ball on the first few minutes, played the ball to Judge, who turned it into the path of Jackson breaking towards the area but Gills keeper Jack Bonham was quickly off his line to block his flick goalwards on the edge of the box.
At the other end, Lee scuffed a shot well wide after latching on to Chambers’s mishit clearance.
Centre-half Wilson wasn’t far away from his first ever Town goal in the 26th minute when he glanced Dozzell’s right-sided corner just past the far post.
In the 23rd minute Jackson teed-up Judge inside the area but the Irishman appeared to have his feet taken away from him as he sought to shoot but referee Christopher Sarginson wasn’t interested. Judge looked in some pain following the challenge but was able to carry on.
The Blues were starting to get up a head of steam and in the 25th minute Edwards was found by a deep cross from the right and hit a low shot through to Bonham, who was untroubled.
Wilson again wasn't too far away from a first Town goal in the 27th minute when he met another Dozzell corner from the right at the near post and sent it across goal and once more beyond the post.
A minute later, Mark Byrne hooked a volley towards goal which was deflected wide after the Blues had struggled to get the ball out of their box.
Following the resulting corner some sections of the home support thought they had gone in front when Thomas O’Connor’s powerful strike from distance looped over Holy and rippled the top of the net, however, having gone over.
Town suddenly found themselves under pressure and in the 31st minute the Gills went even closer to going in front. Lee’s corner was nodded back into the area and Brandon Hanlan’s overhead kick was somehow stabbed wide by Gills skipper Max Ehmer from a few feet.
It was a lucky escape for the Blues but a minute later they took the lead. Jackson and Dozzell exchanged passes on the left and the former Accrington man sent over a deep cross which Vincent-Young met at the far post from where he nodded his first ever goal for Town across Bonham and into the net.
On 38, after Judge had superbly pulled down a ball on the touchline, Jackson did equally well to work himself space for a cross but Dozzell’s first touch let him down and the danger was cleared.
Byrne was shown the game’s first yellow card in the 43rd minute for a late challenge on Skuse, hardly the first overzealous challenge from the combative Gills.
The scoreline remained the same at the break with the Blues good for their lead having had the better of the half against a battling Gillingham side.
Town had dominated the ball, although while rarely looking as fluid as at the MK Dons on Tuesday, and had created one or two openings - but perhaps not as many clear-cut chances as manager Lambert would have liked - with Vincent-Young getting forward and taking his opportunity brilliantly.
At the other end there had been a couple of scares, most notably when Ehmer missed seconds before the goal.
Gillingham: Bonham, O’Keefe, Ehmer (c), Ogilvie, Hanlan, Fuller, Byrne, Lee, Jakubiak, O’Connor, Tucker. Subs: Walsh, Hodson, Ndjoli, Mandron, Charles-Cook, Cissé, Pringle.
Town: Holy, Woolfenden, Chambers (c), Wilson, Vincent-Young, Skuse, Downes, Edwards, Dozzell, Judge, Jackson. Subs: Norris, Norwood, Nolan, Garbutt, Georgiou, Huws, Keane.