Last term was one to forget for Chris Turner's men, who finished well adrift at the bottom of League One after a season of transition.
But Flynn, who captained the club into the old First Division under Dave Jones in 1997, thinks that County are now through the worst of their troubles.
"There's been a massive change in personnel at Stockport this season, but I believe they have the ability to push for a top spot," Flynn said.
"I'm looking at some of the signings and see the club has strengthened. I am quietly confident they will do well.
"They've brought back Rob Clare, who is an excellent young defender.
"When I was with him at the club a few years ago, there was talk of him moving to a Premiership club, and he had just broken into the England Under-21 side.
"He's a fans' favourite and he'll be good for the club this season.
"There are a lot of good players that have gone, but you can look at it both ways, especially now that the Stockport Supporters Trust have taken over the running of the club.
Flynn also believes that the quality of youngsters coming through the ranks at Edgeley Park bodes well.
"In Michael Raynes and James Spencer, we have two excellent young players. Ideally it would be nice to keep the pair, but if it's true about the amount of money that has been rumoured to have been offered for them, then I can see it as beneficial that both players are sold.
"If the club got in the region of £400,000 to £500,000, then Chris Turner could buy in some new players and that would probably be more beneficial.
"I'm sure County will have a very good season. I do sense there is a fresh optimism at the club."
ONE TO WATCH: "James Spencer just seems to get better and better. If he were to go to the Premiership, then the guidance he would get would make him into an even better player."
PREDICTION: "I think Stockport will finish in the top 10 and be pushing for a play-off place."
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