Gillingham's Republic of Ireland Under-21 striker scored either side of half-time to inflict Huddersfield's third straight league defeat.
The Terriers sent Birmingham City crashing out of the FA Cup last weekend, but the Gills came from behind to claim only their second away win of the season.
The home side went ahead through FA Cup match winner Chris Brandon, who fired home after Simon King gave the ball away to Luke Beckett.
Huddersfield failed to build on the lead and Gillingham levelled through Mulligan on the stroke of half-time.
The impressive Adam Miller sliced open the Huddersfield defence and Mulligan wrong-footed Nathan Clarke and planted a shot past Matt Glennon.
Huddersfield should have been back in front on the hour when Brandon's superb through ball left Beckett with only Simon Royce to beat but he rolled his finish wide.
That proved the crucial turning point and when Clarke brought down Miller, Mulligan stepped up to score from the penalty spot.
Mulligan celebrated by stripping his shirt off and was booked by referee David Foster.
Mulligan's strike partner, Huddersfield-born Delroy Facey who started his career at the Galpharm Stadium, smashed home the third eight minutes from time.
Man of the match Miller blotted his copybook in stoppage time when he was issued with a straight red card after a nasty foul on Frank Sinclair.