Sam Jones netted his first goal for the club as Town returned home with a hard fought point at Maidenhead, who started the afternoon in the Play-Off positions.
The number ten headed Alex Bradley free kick in at the back post after just nine minutes, though Town's lead was cancelled out 13 minutes later by Shamir Fenelon's long range strike.
Mark Beck thought he had won it for Town who finished strongly, but saw his 84th minute header cleared off the Town, leaving Town with a point to show for their trip to York Street.
Simon Weaver made two changes from Saturday's goalless draw against Boreham Wood as Jon Stead returned from suspension, while Jack Diamond made his first start for the club.
Town started the afternoon well, forcing a good save from Taye Ashby-Hammond when Alex Bradley took aim from the edge of the box.
The on-loan Lincoln midfielder did manage to beat the 'keeper with his next effort, but saw his first time attempt bounce back off the post, rather unfortunately!
Town grabbed a deserved lead in the ninth minute when Bradley lofted a free kick to the far post that Jones was able to bundle over the line for his first Town goal.
The lead lasted until just the 22nd minute though when Fenelon unleashed an unstoppable effort into the top right corner to level.
The tie was almost turned on it's head in strange circumstances when Will Smith's clearance bounced back off George Smith and almost ended up in the back of the net, but fell wide of the goal.
The goal had given the hosts a lift, with James Belshaw required to keep the score level in the 33rd minute, keeping out Ryan Upward's goalbound strike in what was the last chance of an entertaining first half.
Brendan Kiernan had Town's first attempt of the second half, cutting in and hitting the target after Jones had won possession and found his teammate on the right wing.
With the home defence showing no signs of creaking, Weaver introduced a new strike force in Mark Beck and Jack Muldoon, though it was Diamond who created the next opportunity, picking out Ryan Fallowfield at the back post, though the full back was unable to bundle Town back into the lead.
Beck thought he had won it for Town in the 84th minute when he headed Kiernan's deep cross down towards goal, only for Alan Massey to prevent the ball going over the line at the last second!
Town's final chance fell to Kiernan in the 88th minute, who showed great energy to burst through on goal, but was twice denied by the impressive Ashby-Hammond.
Harrogate Town: Belshaw, Fallowfield, G Smith, Burrell, Jones (Muldoon 62), Kiernan, Bradley, Stead (Beck 67), Hall, W Smith, Diamond (Thomson 73)
Subs not used: Thomson, Cracknell, Brown
Goals: Jones 9
Booked: Diamond, Thomson
Maidenhead: Ashby-Hammond, Steer, Ellul (Clerima 51), Fenelon, Comley, Cassidy, Mensah (Akintunde 69), Nana-Twumasi, Upward (Davies 81), Massey, Smile
Subs not used: Dunne, Whitehall
Goals: Fenelon 22
Referee: E Swallow