Mark Beck's third goal in two games and a world class save from James Belshaw secured three points for Simon Weaver's men against Maidenhead at The CNG Stadium; moving Town up to sixth in the National League table.
A sixth win in the last nine games and a fourth clean sheet in the last five read for impressive stats with Town now looking to carry on their impressive into the final nine games of the season.
Weaver named the same side for the fifth game in a row, while there was a place on the bench for midfielder Joe Leesley.
The Magpies had the first sight of goal after just six minutes when, after some good pressure, the visitors won themselves a corner and picked out the tall Ayo Obileye who volleyed at goal, but his effort flew over the bar.
Minutes later Harrogate had their first attempt, Captain Josh Falkingham ran at the Maidenhead defence and let fly from the edge of the box, a smart left footed shot from a right footed player, but the visiting keeper Carl Pentley was equal to the effort.
Maidenhead looked like a strong physical side in the opening exchanges, with Obileye man marking the inform Beck right from the off after his brace against Braintree the weekend before.
Both teams struggled to get going in the very wet conditions, Harrogate were moving the ball efficiently across the surface, but couldn't find a final killer touch with Callum Howe and Jack Muldoon missing the target on two separate occasions.
In the 33rd minute Kevin Langmead latched onto the end of a perfectly weighted cross by Jack Emmett but unfortunately the Town defender could only add to the home sides shots on target rather than make a mark on the scoreboard.
Moments later, Harrogate continued a good run of attacking play as Emmett was picked out Ryan Fallowfield, but he couldn't guide his effort on target.
As the board went up for added time, Harrogate had a glorious chance to open the scoring after winning a freekick on the left-hand side as Thomson was fouled by Seth Nana-Twumasi.
Thomson stepped up and the whipped a cross into the box which Warren Burrell rose highest to meet but his header skimmed the outside of the post.
Town opened the scoring In the 53rd minute when Thomson whipped in a cross to the far post which picked out the rising Beck who headed his effort across goal and into the back of the net; The striker's ninth goal of the season.
In the 64th minute Maidenhead should've been on level terms when Ryan Upward rose like a salmon and headed the ball at the Harrogate goal only for Belshaw to pull off an incredible one handed save which tipped the effort onto the bar to deny the visiting side.
Harrogate looked lively as the second half went on, Beck was continuing to impress with Emmett and Falkingham displaying a wide range of attacking passing while the home side continued their search for a second goal.
Five minutes before the tireless Jack Muldoon, who had been running hard all afternoon had a chance to double the home sides lead as Thomson whipped in a cross to the near post which Muldoon flicked on towards goal, but he couldn't guide his effort on target.
Town held out for the remainder of the game and secured the three points to see them move up to sixth in the National League table.
Harrogate Town: Belshaw, Fallowfield, Falkingham, Howe, Burrell, Thomson, Emmett, Beck, Langmead, Kerry, Muldoon
Subs not used: Senior, Leesley, Cracknall, Agnew, Williams
Goals: Beck 53
Maidenhead: Pentney, Clerima, Steer, Obileye, Comely (Odametey 73), Nana-Twumasi, Clifton, Akintunde (Worsfold 61), Upward, Massey, Nombe (Kelly 61)
Subs Not used: Alves, Owusu
Booked: Upward, Steer, Nana-Twumasi
Referee: D Middleton
Report by Isaac Martin