Manager Stan Ternent recorded a victory in his first encounter with the club he supported as a boy and left at the end of last season.
But more importantly, the win helped ease Gillingham's relegation worries.
They had the better early chances and Jonathan Douglas missed a gilt-edged opportunity on 12 minutes. Released into the box by a slide-rule pass from Nicky Southall, the on-loan Blackburn man screwed his right-footed effort horribly wide of the far post with time and space on his side.
Burnley's James O'Connor then found his way into the referee's book after he was denied a penalty.
The midfielder went down in the box under a challenge from Gills captain Paul Smith but his appeals for a penalty were waved away.
O'Connor then spent fully 60 seconds chasing referee Mr Olivier around the pitch to berate him before finally landing himself a yellow card.
It was an entertaining game with Gillingham, fighting for their lives, much the more positive. Mamady Sidibe almost gave them the lead on 35 minutes with a towering header from Southall's corner, but it flashed past the upright.
After taking the lead, Gillingham's confidence grew and they carved Burnley's weary defence apart almost at will. Their players adopted a shoot on site policy and Southall nearly found the target with a volley over his shoulder on the turn - it was champagne stuff.
Henderson should have made the game safe on 69 minutes after another rapier break from the home side.
Sidibe broke down the right and played an inviting ball across the six-yard box as the nine-goal top scorer came steaming in towards goal.
Sniffing glory, Henderson made a complete hash of the chance, stumbling over the ball and falling over without so much as forcing a save from relieved Clarets keeper Brian Jensen.