Huntington was well placed at the back post after an hour to head home Chris Humphrey’s cross for his first goal since December 2013.
The scoreline could have been far more comfortable, with Preston hitting the woodwork no less than four times – the first of which came from Joe Garner.
Top scorer Garner headed against the crossbar after 11 minutes and shortly before Huntington’s effort both Jack King and Callum Robinson struck a post.
Paul Gallagher almost made the game safe five minutes from time, but his fizzing effort cannoned off the crossbar while hosts Gillingham had little sight of goal.
The closest they came was through Brennan Dickenson, but he was also denied by the frame of the goal with a 20-yard effort.
Preston goalkeeper Jamie Jones did earn his keep though, denying Danny Kedwell and Cody McDonald, before Gallagher cleared John Egan’s header off the goal-line to secure the win.