RUNCORN paid for a lapse of concentration although they had 81 minutes to put it right at Wetherby Road on Saturday.
Marc Smith's ninth-minute goal was enough to confirm Alvin McDonald's first defeat since assuming the Linnets' hot-seat - after a run of five unbeaten Nationwide North League games.
Defeat was a painful lesson for the Linnets, who made the mistake of switching off from a corner after Tony McMillan had saved well from Paul Shepherd.
Big striker Smith, earmarked by McDonald as a player Runcorn had to watch, exploited slack marking to head home the Lee Philpott's corner.
There was little to choose between the teams and it was always a fear that Runcorn's early error might ultimately cost them.
But they did their best to turn things around.
Harrogate's skipper Paul Pettinger kept them in front with three fine saves, including one from substitute striker Carl Rendell.
A bright spot for the visitors was the promise shown by midfielder Tom Fields, who came off the bench for his first appearance.
The Linnets have an incentive to return to winning ways tomorrow when they travel to Barrow for a second-round Conference National Cup tie with the prize for the winners being an attractive home game against Carlisle United.
Manager McDonald will be hoping defender Robbie Moore can shrug off an ankle injury in time for kick-off.
HARROGATE TOWN: Pettinger, Wood, Barnard, Sturdy, Haran, Philpott, Dunning, Krief (Blackstone), Smith, Holland (Donaldson), Shepherd. Subs: Black, Hunter, Buxton.
RUNCORN FC HALTON: McMillan, Carragher, McGinn (Fields), Moore, Robertson, Ness, Brown, Parle (Rendell), Young, Byrne, Courtney. Subs: Durkan, Nolan, Wright. ..