Goals from Josh Morris and Paddy Madden were the difference for the Cod Army, Madden striking from the spot.
Morgan Boyes also came in for his first start in a Fleetwood shirt since signing on a season-long loan from Liverpool this week.
County had the first chance of the game, Richard Bennett unable to make it count.
The next chance fell the way of Fleetwood and Madden, last season's top scorer getting through one on one but his shot was thwarted by Ben Hinchcliffe.
Town would have the lead shortly after however, Madden and Ched Evans linking up before the latter played in Josh Morris who find the corner.
Before the break the Cod Army doubled their lead, Danny Andrew - fit after a minor knock kept him out of the Carlisle United friendly - crossing into the area for Wes Burns who was brought down; Madden converting the spot kick, sending the goalkeeper the wrong way.
In the sceond half Town came forward again, a trialist whipping a ball into the box which was cleared to Burns outside the area who fired over the bar.
With a raft of changes on the hour mark, Fleetwood did keep pushing, Harvey Saunders chasing down a backpass and getting something on the goalkeeper's clearance, almost turning the ball into the net.
Fleetwood XI: Trialist (GK), Trialist, Andrew, Boyes, Holgate, Burns, Evans, Camps, J.Morris, Coutts, Madden.
Fleetwood bench: Trialist (GK), Sowerby, Biggins, Hill, Baggley, Johnston, Matete, Rydel, Saunders, S.Morris.
Stockport XI: Hinchcliffe (GK), Minihan, Kitching, Hogan, Palmer, Stott, C.Jennings, Maynard, Bennett, Rooney, Reid.
Stockport bench: J.Jennings, Trialist, Keane, Downing, Thomas, Coleman, Turnbull, Walker, Stephenson, Bell, Curran.