Town exited the FA Trophy at the last 16 stage courtesy of an impressive four goal performance from Stockport County.
The Hatters confirmed their tenth straight victory courtesy of goals from Matty Warburton, Adam Thomas and a brace from former Town man Frank Mulhern.
Simon Weaver named Deadline Day signing Jack Senior on the bench, while naming the same starting eleven that were victorious against Hartlepool United in front of BT sport cameras two weeks ago at The CNG Stadium.
The winter sun was beaming down as the visitors got the game underway with the opening ten minutes being a cagey affair with neither side really getting a foothold in the game.
Weaver's men were passing the ball around and making the visitors chase the game, but the home side couldn't create the game's first clear-cut chance.
In the 17th minute, Harrogate attacked through Jack Emmett who whipped a dangerous ball into the box which caught Stockport midfielder Jordan Keane, who tried to clear but ended up steering it into his own net.
Town's lead wouldn't last long though as, in the 21st minute, Darren Stephenson held up play well and teed up Adam Thomas who fired low at the Harrogate goal and found the equaliser.
Just over a minute later Stockport took the lead, a defensive mistake allowed Mulhern through on goal who then bent his effort past James Belshaw, capping a manic five-minute period.
After taking the lead Stockport looked like a completely different side, despite beginning the game looking like they were going to stand off Town and take their chances on the break, after the quick-fire goals they grew in confidence and started to attack the Harrogate defence.
With the game edging towards half time Harrogate were still very much in the game, every time they attacked the Hatters defence looked vulnerable and on one occasion a counter attack from the home side resulted in George Thomson firing a rocket of an effort at Ben Hinchcliffe, but the keeper was equal to it.
In the 48th minute Stockport grabbed their third of the afternoon, Warren Burrell tried to pass the ball back to Belshaw but it fell short and was picked up by Matty Warburton who rounded the Harrogate keeper and slotted home his fifth goal in the last two games of the competition and his 22nd of the season.
Despite the two goal deficit, Town were still continuing to attack the Stockport goal.
In the 68th minute after some good passing play in the middle of the park captain Josh Falkingham managed to feed Thomson who got an effort away at home, but he couldn't squeeze his effort towards the inside of the far post after a great save from the visiting keeper.
In the 73rd minute Weaver introduced Aaron Williams to the action and it almost payed off instantly, after a goal mouth scramble Williams pulled off an acrobatic effort at goal but he couldn't guide his effort either side of Hinchcliffe.
Despite Town looking they were improving and growing back into the game, Stockport grabbed their fourth of the afternoon.
Striker Mulhern picked up his second when Thomson lost possession of the ball on the halfway line which released Mulhern who then rounded Belshaw and squeezed his effort through the Town defenders on the line.
Town weren't down and out just yet though, they continued to attack and in the 88th minute grabbed a goal back thanks to Thomson.
Falkingham released Fallowfield who then picked out Thomson in the middle, the midfielder making no mistake and slotting home, though it turned out to be a consolation only as Town exited the competition.
Harrogate Town: Belshaw, Fallowfield, Falkingham, Howe (Senior 84), Burrell, Thomson, Emmett (Leesley 63), Beck, Kerry, Muldoon (Williams 73), Kitching
Subs not used: Cracknell, Woods
Booked: Kitching
Goals: Keane OG 17, Thomson 88
Stockport County: Hinchcliffe, Minihan, Duxbury, Keane, Palmer, Baines, Thomas, Walker, Mulhern (Kirby 83), Warburton (Cowan 66), Stephenson (Turnbull 75)
Subs not used: Ormson, Osbourne,
Booked: Baines
Goals: Thomas 21, Mulhern 22, 80, Warburton 48
Referee: M Woods
Attendance: 1142
Report by Isaac Martin