McGowan made seven birdies and chipped in for eagle at the par-five eighth on the new course layout in Denmark.
The Englishman holds a slim advantage over Ewen Ferguson, Matthew Southgate, Justin Walters, Rasmus Hojgaard and Marcus Helligkilde, who had been tied for the lead with 63s until McGowan's big finish.
Craig Howie, Francesco Laporta, Rikard Karlberg, Richard Mansell, Soren Kjeldsen, and Nicolai von Dellingshausen are in a group two shots off the pace.
"I'm very happy with that round, hit the ball close early doors and left myself a few birdies from four or six feet or so," McGowan told the DP World Tour website.
"I felt like it's been getting better the last few weeks but it's nice to finally put a round together and hopefully I can keep it going for the next three days."
Ferguson, a two-time winner this season, said he drew inspiration from playing with former Ryder Cup captain Thomas Bjorn and fellow Scot Robert MacIntyre.
He said: "It was the first time I'd played with Thomas and obviously I've played with Bob since I was, well, in nappies, so it was a good, fun group.
"Thomas was saying he couldn't believe how much us Scots moan, but I think he matched us pretty well!
"Obviously playing with those two drew a bit of a crowd so it was exciting being out there. I really enjoyed it and tried to make sure I embraced it."