Town could not put an end to Wrexham's unbeaten home record on Tuesday night and were eliminated from The FA Cup at the 4th Qualifying Round stage courtesy of a 2-0 defeat.
After 242 minutes of goalless action between the sides this season, Akil Wright broke the deadlock in style with an acrobatic near ppost finish.
Another clinical finish from Luke Young in the 67th minute ended all hopes of a Town comeback and ensured Simon Weaver's side suffered a second defeat of the season.
Weaver made two changes from Saturday's draw as Callum Howe was deemed fit enough to start, alongside Liam Agnew, as Ryan Fallowfield and George Thomson dropped to the bench.
Town's number 12 looked lively early on down the right hand side, but it was Wrexham who had the early attempts on goal with Luke Young shooting wide before Akil Wright's diving header flew wide.
Jack Emmett had a low shot saved at the other end, before a goalmouth scramble almost saw Town claim an early advantage.
Joe Leesley's free kick was attacked by Liam Kitching and somehow kept out on the line with Aaron Williams among a number of bodies throwing themselves towards the loose ball.
With eight minutes to go until the break, Josh Falkingham won possession in midfield and launched an attack down the left, though Rob Lainton was perfectly positioned to deny Williams at the near post.
Three minutes later it was the turn of James Belshaw to keep the tie goalless as the stopper kept out Jordan Maguire-Drew's free kick that looked to be dipping just under the cross bar.
With nothing to seperate the sides in the early exchanges of the second half, the hosts introduced Mike Fondop up front who seemed to galvanise the side.
Six minutes after the striker's introduction Wrexham took the lead as a corner to the near post was acrobatically turned in by Wright in what was his first goal for the club.
The hosts had the wind in their sails and were only denied a second minutes later by Kelvin Langmead who threw himself in the way of substitute Fondop's shot.
With 14 minutes remaining Wrexham doubled their lead as the impressive Fondop held up the play and teed up Young who despatched the ball first time into the bottom right corner.
Warren Burrell had the chance to reduce the deficit two minutes later, but could only guide Leesley's free kick into the arms of Lainton.
Substitute Mark Beck was next to go close, but could only head Jack Muldoon's driven cross into the arms of a grateful Lainton.
With Town piling men forward, space was opening up at the other end, space that Rekeil Pyke almost exploted with a curling effort late into the night.
Despite eight minutes added time, Town couldn't break down a Wrexham defence that has only conceded three goal at home all season and saw their FA Cup run come to an end.
Harrogate Town: Belshaw, Falkingham, Howe, Burrell, Emmett, Leesley, Thewlis (Muldoon 67), Agnew (Kerry 60), Langmead, Williams (Beck 56), Kitching
Subs not used: Fallowfield, Thomson, Cracknell
Booked: Langmead, Howe, Emmett
Wrexham: Lainton, Roberts, Jennings, Young, Pyke, Carrington, Maguire-Drew (Fondop 56), Walker, Wright (Rutherford 71), Beavon (Burgess 92), Lawlor
Subs not used: Dibble, Holroyd, Deverdics, Tharme
Goals: Wright 62, Young 76
Referee: D Middleton