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Early goals proved enough for Gills to take the points at Northampton on Tuesday night.
Josh Parker and Tom Eaves netted the goals for Gillingham after a dominant first half.
Ash Taylor halved the deficit for Northampton 10 minutes after the restart but the Gills hung on to claim the win.
Reaction: Magnificent first half showing delights the manager
Gills boss Steve Lovell made two changes to his starting XI and switched formation, playing 3-5-2, as Connor Ogilvie and Ben Nugent returned to the team.
It proved a great call as the visitors limited Northampton to only half-chances during the first 45 minutes, Daniel Powell on the end of most efforts without success.
Gillingham took the lead after just six minutes, Parker driving at a shaky defence and the unleashing a shot from 20 yards that flashed across keeper Richard O’Donnell.
Parker came close to turning provider six minutes later, peeling off his marker to get on the end of Tomas Holy’s ball forward before crossing for Eaves, who fired over.
It wasn’t long before Eaves had his goal. Luke O’Neill picked him out with a low cross and the Gills striker slid in to convert the second.
The Gills front-two were bossing the home defence and continued to threaten for the remainder of the half. Parker had the ball in the net again, heading home another superb O’Neill cross, but the offside flag was raised.
Parker had an early second-half shot blocked but the home side got themselves back in the game, 10 minutes after the restart, when Taylor flicked on Matt Grimes’ free-kick beyond Holy
The Gills remained under pressure, Holy being called upon to save one-handed from sub Gboly Ariyibi and then saving the follow-up. Joe Bunney also fired an effort wide.
Lovell looked to stem the home pressure by switching back to 4-4-2 with Lee Martin and Scott Wagstaff introduced from the bench.
Martin won a corner straight after going on and moments later shot narrowly wide.
Hildeberto Pereira, Northampton’s half-time sub, put a chance over the bar as the home side ended a brief spell of Gills pressure with a quick break.
John-Joe O’Toole went close for the hosts but Eaves had a great chance to restore the two-goal advantage, heading wide from close range after Parker’s header had been well saved by O’Donnell.
Pereira was sent off after the final whistle for Northampton, for dissent.
Northampton: O’Donnell, Moloney, Taylor, Foley (Pereira 46mins), Powell (Mathis 83mins), Hoskins (Ariyibi 57mins), Long, O’Toole, Grimes, Turnbull, Bunney. Subs: Cornell, Barnett, McWilliams, Crooks.
Gillingham: Holy, Ogilvie, O'Neill, Nugent (Martin 71mins), Zakuani, Ehmer, Byrne, Hessenthaler, Reilly (Wagstaff 71mins), Eaves, Parker. Subs: Hadler, Garmston, Moussa, List, Wilkinson.
Attendance: 5,123 (419 away)