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Harry Lennon scored an injury-winner for ten-man Gills against Scunthorpe.
Justin Edinburgh’s side fought back from a one=goal deficit to win Tuesday night’s game at the death.
Scott Laird had given Scunthorpe a deserved second-half lead, but Brennan Dickenson headed table-topping Gills level.
Gillingham finished the game with 10 men after Josh Wright was red carded for a foul on Paddy Madden, but Lennon bundled home a stoppage-time winner.
The Gills had an unbeaten home record to protect, with they did in the end, against a confident Scunthorpe side who arrived at Priestfield boasting three wins from their last three.
Gillingham made two changes to their starting 11 and there was a new face on the bench, with 16-year-old first year scholar Noel Mbo making up the numbers.
The young striker was in to bolster Gillingham’s forward options due to injuries to Luke Norris and Cody McDonald.
Gillingham started Tuesday’s game brightly enough but soon faded, with Scunthorpe having the better of the chances in the opening half.
Scunthorpe’s experienced forward Gary McSheffrey was a constant menace during the first half, with his delivery from set-pieces also posing problems.
Stuart Nelson made a block from one of McSheffrey’s corners late in the half but didn’t know too much about it, as the ball was whipped in at the near-post.
John Egan had Gillingham’s only on-target effort of the first period, which was blocked, while Jake Hessenthaler headed a chance wide.
Scunthorpe’s Murray Wallace glanced a header wide for the visitors from another dangerous set-piece and Scott Wiseman put another chance wide as the Gills ended the half thankful to still be on level terms.
Edinburgh showed what he thought of the half by making two changes. Jermaine McGlashan and Brennan Dickenson replaced Hessenthaler and Ben Williamson.
Despite the changes Scunthorpe went ahead, Laird smashing in a cross from Wiseman in the 53rd minute.
Gillingham levelled the scores just six minutes later as Dickenson rose to head home Bradley Dack’s corner, claiming his first goal of the season.
He almost scored a spectacular second with 66 minutes gone, creating space with his first touch and then volleying just wide with his second from 25 yards.
Scunthorpe remained a threat, as the Gills struggled to dictate the game, and Laird delivered a tantalising ball that just eluded the touch of three visiting players.
Wright’s dismissal came with 10 minutes left and it was harsh. Referee Lee Swabey had already incensed the Gills with several controversial decisions, but his red card for the midfielder surprised most inside Priestfield, with a challenge that deserved a yellow at best.
Scunthorpe pressed late on with the extra man. Jack King fired a chance narrowly over and Aaron Morris had to make a great block to deny Tommy Rowe.
The Gills weren’t finished, though, and Lennon converted a Dack free-kick from close-range. But victory was only guaranteed with a point-blank save with the final play of the match, as Nelson denied Wallace’s close-range effort.
Gillingham: Nelson, A Morris, Garmston, Lennon, Egan, Wright, Hessenthaler (Dickenson 46mins), Osadebe (Houghton 70mins), Dack, Donnelly, Williamson (McGlashan 46mins). Subs not used: G Morris, Ehmer, Oldaker, Mbo.
Scunthorpe: Daniels, Wiseman, Laird, Mirfin, Madden (Lolley 89mins), Bishop, King, Rowe, Hopper (Van Veen 83mins), Wallace, MacSheffrey (Williams 67mins). Subs not used: McAllister, Anyon, Goode, Clarke.
Attendance: 4,823.