McGowan added a second round of 65 to his opening course-record 62 for a halfway total of 15 under par, with compatriot Richard Mansell and Italy's Francesco Laporta a shot behind.
The 40-year-old, who carded nine birdies and three bogeys, said: "I played pretty solid early doors although I mis-clubbed a couple of times as the weather started getting warmer and I didn't adjust quick enough so I made a silly bogey at six.
"But I bounced back well with a few birdies to close the front nine and then made a couple of silly mistakes on the back nine and a couple of bogeys, but I finished well."
Mansell and Laporta both shot 64 for the second day in succession as the low scoring meant the cut fell at four under par, with Ryder Cup captain Luke Donald missing out by a shot following a 72.
"The course is scoreable, but you've still got to go and do it so I'm happy," said Mansell, who was third in the Omega European Masters last week and fourth in the ISPS Handa World Invitational a fortnight earlier.
"I've had two days bogey free and cut out mistakes, which helps. We've been playing good stuff for a while and when I did have to knock some par putts I rolled them in confidently so if I can keep that going that's a good sign.
"This is why you practise every day and work so hard, to be in contention. If I can keep knocking on the door I'm sure it will open soon."
England's James Morrison is six shots off the lead after equalling McGowan's course record, but revealed a disappointing opening 71 meant he had expected to be making an early exit.
"I played absolutely dreadful yesterday," Morrison explained. "I checked out of my hotel, booked a flight, put my bags in the car. I thought, 'Sod it, I'm out, I'm going home'.
"Shot nine under par this morning and I've got nowhere to stay tonight. Golf's an absolutely stupid game."