No transfer fee is involved for a player who Latics signed for £15,000 from Welsh club Barry Town in the summer of 2002. Flynn would have been out of contract in the summer and Paul Jewell decided not to stand in his way when Gillingham boss Stan Ternent made the approach to take him to Kent.
Jewell told the Evening Post: "Flynny goes with our best wishes because he's been a super lad to have around the dressing room and has played his part here.
"We got him for £15,000 from Barry Town and while he's not been a first-team regular here, we've had our money out of him.
"His contract would have been up in the summer and I couldn't guarantee him a long-term future here, so I wasn't going to prevent him taking up a two-and-a-half year deal with Gillingham.
"It's a free transfer but we will get a good percentage of any deal if Gillingham were to sell him in the future.
"I know Stan Ternent very well and Stan will be a good manager for Flynny to work with.
"This is a chance for him to get established at a Championship club and I'm sure he'll prove as popular down there as he was here.
"I've always thought that Flynny was good enough to play for a lot of Championship clubs and it's just unfortunate he's not been able to quite squeeze his way in at Wigan."
Earlier in the season, the 24-year-old spent five weeks on loan at Blackpool, playing six times before being recalled to Wigan because of an injury crisis.
He's been in and around the squad ever since, but his only starts came in the FA Cup at Derby last month and the league meeting with Watford.
Competition in the centre of midfield is strong at the moment, with Jimmy Bullard, Alan Mahon, Gareth Whalley and Andreas Johansson all vying for places.
Jason Jarrett has also returned early from a loan spell with Stoke and will be free to make his challenge after the visit of the Potters to the JJB Stadium on Saturday.
Recent signing Johansson played in the reserves against Tranmere Rovers yesterday afternoon as he stepped up his fitness ahead of a possible first-team debut this weekend.
Assistant manager Chris Hutchings believes the Sweden international could be a vital card in Latics' pack as the promotion battles heats up due to the break in action he had between the end of the Swedish season and him signing for Wigan.
"The fact that Andreas has had a little break might end up being very important because he should be fresher when others are tiring," said Hutchings.
"He gives us several options because he can play in midfield, go up behind one striker or even play as a striker himself. He's looking 100% better than when he first arrived here and has been doing a lot of fitness work with our conditioning coach.
"I'd say he's looking as sharp as the rest and he just needs matches now to get him fully ready."
Johansson played the full game yesterday which ended in a 2-2 draw, youngsters Luke Joyce and Sam Lichfield on target.