A Mark Beck brace ensured Town progressed to the first-round proper of the Emirates FA Cup for the first time in seven years.
Town entered the 2019/20 FA Cup in the fourth qualifying round in a Yorkshire derby contest against Halifax, a side Town defeated only three weeks ago thanks to a 90th minute winner from Beck.Town started on the front but it was Halifax who had the first opportunity with Toby Sho-Silva breaking free.
James Belshaw did well to close down the angle to force the corner which caused no threat.
Brendan Kiernan was finding joy down the right flank and it was Kiernan's delivery which brought the first goal of the game in the eighth minute.
The ball in was met by Halifax defender Josh Staunton who headed against his own cross bar. Beck was first to react and smash home from close range.
Town looked to assert their early dominance with some relentless pressure.
Connor Hall first tried his luck 25 yards out in the 12th minute and then only 60 seconds later, Jack Diamond headed narrowly over following a pinpoint cross from captain Josh Falkingham.
Falkingham was everywhere during the first half and after the 20th minute, he played a great pass to Ryan Fallowfield who was in acres of space down the right.
It looked like either Beck or Jack Muldoon would get on the end of the cut back but neither managed to get contact with the ball.
Despite Town's control of the game, Jerome Binnom-Williams should have equalised for Halifax on the half hour mark.
The left back was all alone only five yards out as a corner was whipped in, however, the defender was unable to make good contact and headed over.
With five minutes to go before half-time, winger Diamond picked up the ball 30 yards out and drove at the Halifax defence. The youngster managed to beat two defenders to create space and fire at the keeper, forcing Sam Johnson to parry as far as Falkingham who couldn't keep his strike on target.
Halifax came out for the second half with a point to prove and it only took 20 seconds for them to equalise, Niall Maher tapping in at the back post.
Town were on the back foot and nearly went behind in the 48th minute after Liam Nolan should have hit the target following his diving header.
Two minutes later and Halifax hit on the break and great ball by Southwell across the corridor of uncertainty nearly found a teammate.
Harrogate did manage to compose themselves and they took advantage with Beck getting his second goal of the game after 54 minutes.
Muldoon found space in the right side of the box, he played a low ball into Beck who hit first time across the Halifax keeper to restore Town's lead.
Ten minutes later and the ball broke for Muldoon down the left, he pulled it back for Diamond who after moving forward a couple steps, hit a powerful strike which looked destined for the top corner. Nathan Clarke put his body on the line to deflect the effort for a corner.
Sho-Silva came close for Halifax 74 minutes in after Jamie Allen put a low ball into the box. The striker fired high over the bar when he should have done better.
By the 80th minute, Halifax manager Pete Wild had made all three substitutes as the home pressed for the equaliser.
Town did well to make sure the final minutes of the game stayed relatively threat free.
Harrogate now have the opportunity to face one of the big guns from the football league, with Sunderland a potential giant killing waiting to happem.
Town: Belshaw, Fallowfield, W. Smith, Hall, G. Smith, Burrell, Falkingham, Kiernan (Thomson 81), Diamond, Beck, Muldoon (Stead 85).
Subs not used: Cracknell, Taylor, Brown, Emmett, Bradley,
Goals: Beck 8, 54
Bookings: Burrell, Fallowfield, Thomson, Diamond
Halifax: Johnson, Duckworth, Binnom-Williams, Clarke, Nolan, Southwell (Allen 68), Sho-Silva, Staunton, McAlinden, Cooper (J King 77), Maher (Earing 79).
Subs not used: Appleyard, Hanson
Goals: Maher 46
Bookings: J. King
Referee: A Miller
Attendance: 1241 (228 away)
Report by Henry Whitaker