Two goals in each half ended the Linnets' nine-game unbeaten start to the season.
This loss also ended their undefeated league run stretching back 29 games to last season – just two games shy of the club record set in 1921-22.
Disappointed Linnets boss Keith Webb said: "We took the game to Harrogate to start with, but once they scored we just fell away.
"We didn't start playing again until they went 3-0 up and our body language wasn't good either. Scott Howie played well and Greg Crane showed plenty of enthusiasm when he came off the bench.
"I'll walk over broken glass for the players if they deserve to be protected but you can't defend the undefendable. That kind of performance was totally unacceptable.
"A few of the players need to realise that they are playing for their careers at the club. We have to learn to handle ourselves at this level and show more resilience. If I have to bring other players in to improve things then I will."
On Harrogate, Webb said: "They were solid, well-organised and more determined than us. You can see why they are in the mix at the top of the table and why they went to Stalybridge Celtic and turned them over."
Jack Defty missed the game due to a jarred knee sustained in Monday's friendly at Wisbech, so Michael Frew was the lone target man in a 4-5-1 formation.
Ben Chapman (injured) and Ben Sedgemore (work commitments) were also missing.
In the even opening exchanges Matty Young hit the away crossbar after Lynn keeper Scott Howie had punched the ball straight out to the lively midfielder.
Scott Mitchell had a shot for the Linnets after good build-up from Julian Joachim, Andrew Fisk and Frew.
But after the first ten minutes Lynn were out of the game, apart from a brief second-half spell, as they were outrun and outplayed.
On 13 minutes James Dean tried his luck with a long-range shot which cannoned back off the defence, and the striker was the first to react to shoot in for a home debut goal.
Harrogate doubled their lead after 22 minutes. Dean and Young set up Darren Dunning to send a tremendous left-footed 25 yard effort that gave Howie no chance.
On the half-hour mark Mark Peters cleared the ball off the line from Michael Roddy when Lynn failed to clear a corner.
In a rare Lynn attack Charlie Defty had a shot blocked for a corner.
Lynn boss Keith Webb introduced Greg Crane at half-time to bolster the defence.
In the opening minutes of the half the hosts' striker Jamie Smith missed a good chance, shooting wide when he should have done better.
Frew cleared the bar on 53 minutes, and soon afterwards Lynn midfielder Mark Camm pulled up and was stretchered off.
Lynn switched to 4-4-2, with Joachim partnering Frew.
On 61 minutes The Walks outfit conceded a bad third goal when Young picked the ball up in the centre circle in his own half and was allowed to race through the middle past a couple of half-hearted challenges and place the ball past Howie.
After Danny Bloomfield came on, Lynn enjoyed their best spell.
Frew, plus subs John Turner and Crane, all had shots saved – their first efforts on target of the game. Later on a Crane header hit the post.
If not for the heroics of Howie, Lynn would have conceded more as the keeper foiled Smith and sub Richard Marshall.
Harrogate ensured Webb suffered the biggest league margin of defeat in his Lynn career to date with the fourth goal deep in injury time.
Dean laid the ball off to Dunning, who crossed from the left for the impressive Young to unleash an unstoppable volley from the edge of the area.
|Harrogate: Provett, Toulson, Smith (Reay 86), Ingram, Killock, Peat, Young, Dunning, Dean, Holland (Marshall 73), Roddy. Subs (not used): Lowe, Gray, Hedge.
Goals: Dean (13), Dunning (22), Young (61, 90).
Lynn: Howie, C. Defty (Crane 45), Smith, Peters, Weaver, Camm (Turner 57), Joachim (Bloomfield 65), Fisk, Frew, Mitchell, Francis. Subs (not used): Kelly, Murray. Booking: Fisk.
Referee: R. Clark (Morpeth). Attendance: 548. MoM: Scott Howie.
Stats, Lynn first: shots on target 4, 12; off target 4, 6; corners 11, 6; offside 2, 3; free-kicks 11, 8.