Fitzpatrick, brother of former US amateur champion and current European Tour player Matthew, shot 69 77 at Wallasey GC.
He is nine back of McGregor Trophy halfway leader, Ham Manor’s Charlie Strickland who was on seven-under 137 (69 68) to lead by three from Dunston Hall’s Toby Briggs (72 68).
Fitzpatrick was two under through the turn in his first round and then moved four under after birdies at 10 and 14, but he dropped a shot at 15.
In round two, he was out in only one over, but a bogey at 11 was followed by a double at the 544-yard par-5 13th.
He immediately recovered one of those at the next, but had two more dropped shots in a homeward 40.
His Hallamshire club-mate Barclay Brown is tied 20th (71 77) as is Daniel Bradbury (Wakefield), who carded 76 72.
Brown was out in two under in his first round, but wuffered a double bogey at 10. He negated its effects with birdies at both 12 and 14, but dropped a shot at the 18th. In his 77 he had five bogeys with the rest all pars.
Bradbury had only three pars in an outward nine in his first round that also contained three bogeys and a triple bogey 6 at the 173-yard par-3 fifth, plus two birdies.
He had a more serene back nine, by comparison, with a birdie at 14 and a bogey at 16.
He started with dropped shots at the first three holes in round two, but then eagled the 531-yard fourth hole.
Birdies followed at seven, 13 and 14, a double bogey 6 at the 15th, a bogey at 16 and a birdie at the last.
Charlie Doughtrey (Rotherham) is tied 28th (73 77). He started his opening round with a birdie, but gave it straight back at the second. He did likewise to close the outward half, birdieing eight and bogeying nine.
His birdie at the 10th was followed by a bogey at 11, plus two more at 12 and 13 before he birdied the 17th for his 73.
He then amassed one birdie and six bogeys in his 77.
Three Yorkshire players were unable to make the cut, involving the top 40 and ties who will play the final two rounds today.
Matthew Roberts (Fulford) shot 73 78. He was three under with three birdies in his first round, but double bogeys at 10 and 11 and seven pars produced a 73.
He had a dozen pars and half a dozen bogeys in his 78.
Hessle’s Joseph Allenby shot consecutive rounds of 77. He was out in level par in his first round with a birdie at the seventh and a bogey at the eighth before dropping five more shots coming home.
He featured three birdies in his second round of 77, including one at the last, but had six bogeys and a double at 17.
James Swash (Middlesbrough) shot 77 79. He dropped three shots in his first five holes in round one, but birdied seven and nine to be out in one over. Four dropped shots coming home, including three in a row from the 13th, led to his 77.
He had seven bogeys on day two but birdies proved totally elusive.