Despite a brilliant penalty save from James Belshaw and a goal from second half substitute Mark Beck, a wonderful freekick and a late penalty from AFC Fylde's Danny Rowe condemned town to a defeat at The CNG Stadium.
Simon Weaver made one change to the team that lost out to Yorkshire rivals AFC Halifax on Boxing day, with Kelvin Langmead coming in for Ryan Fallowfield.
Town looked lively in the opening exchanges, with captain Josh Falkingham hitting the post in the third minute.
Playing in very windy conditions it took a few minutes for both sides to get to grips with the weather with the ball hanging up in the air quite a lot.
Towns second chance came in the 12th minute as Dom Knowles whipped in a lovely cross which found Langmead in the middle, but his effort went just wide.
Town needed to be wary of Fylde marksmen Rowe who had already found the back of the net 16 times this season and was making his presence known to the Town defence.
Two chances for Town came in quick succession in the 28th minute, after Tom Brewitt picked up a yellow card and gave town a freekick on the edge of the box, Joe Leesley whipped in the resulting freekick which hit Fylde captain Neil Bryne's leg and smashed against the post.
Liam Kitching then rose highest from the resulting corner but couldn't keep his effort under the bar.
AFC Fylde's first real chance came in the 32nd minute, Andy Bond broke free and found Rowe in the middle, but the marksmen couldn't get his effort on target and fired it at the crossbar.
Nearly 10 minutes later Rowe had another chance to break the stalemate, after been picked out on the edge of the box, the striker hit a sweet strike towards goal but couldn't keep his effort under the bar.
AFC Fylde got the second half underway and broke the deadlock in the 47th minute, Harrogate conceded a freekick around 30 yards out, of which Rowe stepped up and bended a lovely effort past the Town wall and into the top left-hand corner beyond Belshaw.
Town weren't down and out just yet though, in the 54th minute after a good run from Leesley wins Town a corner, Leesley then balls whipped into the middle and lands on the head of Warren Burrell, but he can't guide his effort under the bar.
In the 68th minute AFC Fylde missed a huge opportunity to double their lead, after Nick Haughton broke through the Town defence, he was brought down by captain Falkingham in the penalty box, resulting in the referee pointing to the spot.
Rowe then stepped up and blasted his effort at goal, but stopper Belshaw was equal to it, pulling off a terrific save to keep any hopes of Town getting back into the game alive.
Town were really upping the pressure in the closing 15 minutes of the game, Lloyd Kerry broke through and was fouled by Francis-Angol resulting in a freekick at the edge of the box.
Resulting was a rehearsed set piece routine from substitute George Thomson and Leesley, but Leesley's couldn't guide his effort past the wall.
Town's persistence would soon pay off, the equalising goal came in the 82nd minute courtesy of substitute Beck.
Beck picked up the ball then swivelled in a packed penalty area and smashed his effort into the roof of Jay Lynch's net to equalise.
Despite Town's resurgence into the game, in the 90th minute Fylde substitute Serhat Tasdemir broke through the Town defensive line and was brought down by Burrell and the Referee pointed to the spot again.
Rowe stepped up again, but didn't make the same mistake twice, blasting the ball past Belshaw, with Kitching receiving two yellow cards for descent in the aftermath of the game.
Report by Isaac Martin
Harrogate Town: Belshaw, Burrell, Howe, Langmead, Kitching, Falkingham, Kerry, Woods (Thomson 67), Leesley, Knowles (Williams 70), Muldoon (Beck 57)
Subs: Cracknell, Emmett
Booked: Leesley, Falkingham, Burrell, Kitching
Sent off: Kitching 91
Goals: Beck 82
AFC Fylde: Lynch, Francis-Angol, Byrne, Bond, Croasdale, Rowe, Philliskirk (Tunnicliffe 60), Gnahoua (Birch 94), Burke, Brewitt, Haughton (Tasdemir 88)
Subs: Green, Williams
Booked: Brewitt, Croasdale
Goals: Rowe 47, 92 (p)
Referee: P Gibbons