The Premier Division bookies favorites showed their class by eventually overcoming a gallant performance by the Blues.
A fairly even opening to the first half saw few opportunities, but it was the visitors who took the lead of 25 minutes. From a corner the ball ended up in the net off the head of FC's centre back Andy Pearson.
Late in the first half, Blues forced a couple of successive corners which came to nothing. A free kick awarded just outside the box saw Mike Aspin curl it just wide of the post.
Half time - Clitheroe 0 FC United of Manchester 1
Both teams made substitutions at half time and it was the visitors greater experience from the bench which made the difference.
Matt Green made an excellent save from Mike Norton on 52 mins and Blues had the ball in the net on 59 mins, when a nice through ball across the goal from James Walker was finished by Ross Dent. Frustratingly for the players, the assistant referee had flagged for an earlier offside.
However, it wasn't long before the Blues levelled the scores when FC's sub keeper Nick Culkin couldn't hold Dent's shot and Peter Dunkerley pounced to convert the rebound.
Just three minutes later FC re-took the league through former Accrington Stanley striker Craig Lindfield and from then on they took control of the game. A James Walker header and a decent effort by Liam Hoyle were the Blues best efforts towards the end of the game.
Matt Green also made another great save from Jerome Wright's half volley on 72 mins.
FC wrapped up the game with two fine strikes by last season's top scorer Tom Greaves on 84 & 86 minutes.
Clitheroe line up: Green, Aspin, Walker, Brady, Mercer, Lynch, Potter, Bonaminio, Burns, Hoctor, Garner. Subs used; Wood-Townend, Freeland, Dent, Byrom, Dunkerley, Mulkerrin, Hoyle.