The Hatters suffered a fourth consecutive home defeat as Braintree Town took all three points thanks to three second half goals, substitute Alex Kenyon's late header being just a consolation.
Darije Kalezic named all four of his new signings, Keiran Charnock, Danny Schofield, Lee Bullock and Javan Vidal, in his starting line up, Jordan Fagbola, Alex Kenyon, Sam Sheridan and Andy Halls all missing from the side that won at Barrow on Tuesday evening.
Schofield had a hand in County's first chance of the game, flicking on to Mark Cullen after neat play down the left between Danny Whitehead and Jon Nolan, Cullen's shot deflected away by Ryan Peters.
The visitors took an early grip on the half , James Tunnicliffe turning away a goal bound effort from Sean Marks, Charnock heading a free kick clear after a foul by Vidal, Daley having a shot blocked by Sean Newton, before Marks found space in behind the County defence only to head straight at Richard O'Donnell.
Jon Nolan appeared to be targeted by the visitors as he was caught late on a couple of occasions, the midfielder requiring treatment after a late challenge from Peters.
O'Donnell was the busier of the two keepers as he kept out a Kenny Davis effort, Marks tested the County keeper before he made a superb save to deny Dan Holman as the striker was through one on one, James Mulley shooting straight at the grounded County keeper from the rebound.
The visitors earned the first corner of the game in last minute of the half as Peters forced his way through a static Hatters defence, his effort being deflected wide by Newton.
HT: Stockport County 0 Braintree Town 0
Alex Kenyon replaced the injured Nolan for the second half, the midfielder immediately putting pressure on the visitors, Paul Marshall picking up the ball after Kenyon's challenge to feed Cullen, keeper Nathan McDonald quickly off his line to smother the ball.
The visitors took the lead from the keepers throw out, Peters breaking down the right before his neat pass found Marks who laid the ball off to Holman to slot home the opening goal.
Within minutes the lead was doubled as Davis beat a poor offside trap to lob the ball over a stranded O'Donnell who had come out to narrow the angle.
County rallied to force a succession of corners, a Kenyon shot that was deflected wide, and a Cullen shot saved by McDonald the closest attempts.
The game was finished as a contest after Davis slammed home a spot kick awarded after Dean Wells was tripped in the box by Bullock.
Another rally from the Hatters saw a Simon Hackney corner kick deflected onto a post before Kenyon grabbed a consolation , the midfielder arriving to head home from a pinpoint Whitehead cross. McDonald then making a point blank save to deny Hackney after he had beaten the offside trap before the visitors saw out the final minutes to claim the points.
FT Stockport County 1 (Kenyon) Braintree Town 3
Starting XI: O'Donnell, Newton, Vidal, Tunnicliffe (Macken), Whitehead, Cullen, Nolan (Kenyon), Marshall (Hackney), Charnock, Schofield, Bullock.
Subs: Ormson, Kenyon, Fagbola, Macken, Hackney.
ATT: 3,250 (46)