McGowan stands at 6-under-par 136 and is two clear at Quinta da Marinha Oitavos Golfe.
On Friday, McGowan's countryman Nick Dougherty also shot the same number he carded on Thursday, a 2-under 69. That puts him alone in second place at 4-under-par 138.
For the second straight round, the wind was the story as tournament officials could not mow the greens out of fear that the balls would not stay on the putting surfaces in the intense gusts.
McGowan participated in Qualifying School last year as an amateur, but failed to get his card. He is playing this week on a sponsor's exemption and began his second round on the first tee. The Englishman parred his first five holes to stay at 3 under par for the championship.
Due to the demanding conditions, that was enough to keep McGowan in at least a share of the lead. He distanced himself from the field with back-to-back birdies at six and seven and was two clear at minus-5.
McGowan birdied the short, par-3 ninth as held a three-stroke lead at 6 under par. Only one other player could muster any kind of challenge and that was Dougherty, who mixed four birdies and two bogeys to get within two of McGowan.
At the 13th, McGowan once again built the lead to three, thanks to a 15-foot birdie putt. Dougherty, playing several groups ahead of McGowan, traded a birdie and a bogey the rest of the way to get in at minus-4.
Unfortunately for McGowan, he dropped a shot at the par-3 14th to fall back to 6 under par. He recorded four pars in a row to end his round and find himself in unchartered waters.
'This is new territory for me, so we will see how it goes,' he said. 'On the amateur scene I had the lead after 36 holes, but it's different with the pros.'
Benn Barham (67), Stephen Gallacher (71), Raphael Jacquelin (69), Alexander Noren (68) and Graeme Storm (67) are knotted in third place at 3-under-par 139.
Two-time defending champion Paul Broadhurst (71), Richard Bland (69), Luis Claverie (68), Sven Struver (70) and Taichi Teshima (69) shared eighth place at minus-2.
Overnight leader Simon Dyson could only manage a 3-over 74 on Friday and dipped down into a tie for 13th place at 1-under-par 141.
The 36-hole cut fell at 4-over-par 146 and among the notable players who did not make the weekend were David Frost (148), Notah Begay III (150) and Jean van de Velde (154).