Eight months ago they slunk away after a six-goal thrashing. And while this scoreline suggests it was another bad defeat this time around it was somewhat harsh on the Kent club.
City had to come from behind and finally grabbed the points with two late goals - the final one in added on time from substitute Scott Murray.
By then the visitors had pulled off defender Brent Sancho to throw everything into the search for an equaliser knowing they were always open to be caught on the counter strike.
City, as manager Gary Johnson freely admitted, were more than pleased with the win after their pre-match thinking had blown up in their faces.
They had gone into the match with a midfield that had a strange look and feel to it with no-one quite certain who should be tracking back in defence and this cost them a goal.
It was shaped by the sheer speed of Matt Jarvis who streaked down the left flank drawing Liam Fontaine out of position as the defender made a vain attempt to stop him.
When Jarvis got in his cross it was to an unmarked Michael Flynn who thumped a tremendous 20-yard shot into the top left corner.
There was little rhythm to City's early game and they owed their revival to right-back Richard Keogh.
The Irishman was on the edge of the box as the short corner on the right was played in by Alex Russell.
Keogh met it with a right foot volley which went past Kelvin Jack on the bounce at his left post.
City had already amended their starting line-up by moving Phil Jevons into the attack and switching young Jennison Myrie-Williams wide on the left of midfield.
But relieved as they were to go in at the break level, City knew Enoch Showunmi could have scored in added on time to the half but he was denied by Jack's great save.
Gillingham's grip was loosened in the second half as Lee Johnson powered in a shot on the hour which Jack splendidly kept out.
The game was now in the balance and Sancho ought to have put the visitors back in front minutes after Johnson's effort but sent a free header from a corner flying off target.
Showunmi's left foot finally lifted City in front as he took a pass from Jevons before Murray's pace and speed gave the scoreline a comfortable look for City.