Only 10 of the 154 players left in the field are under par as the blustery conditions on Scotland's west coast wreaked havoc with five of the world's top 10 failing to make the weekend.
Lowry leads by two from Justin Rose, who came through qualifying to book his place in Troon, and unheralded Englishman Daniel Brown on his major debut.
The Irishman, who won his sole major at the British Open in 2019, recovered from a dramatic double bogey on the 11th that threatened to derail his charge to post a two under par round of 69.
"To be leading this tournament after two days, it's why you come here," said Lowry.
"The job tomorrow as well is to try to put myself in a position to win this tournament on Sunday."
Lowry was on the charge as he hit the turn in 34 thanks to birdies on the first, fifth and eighth.
The world number 33, though, was rocked as after a wayward tee shot at the 11th, he veered way left into thick bushes.
Remarkably Lowry's ball was found, but deemed unplayable forcing him to play a drop and lose two shots.
He bounced back impressively picking up two shots in the final three holes.
World number one Scottie Scheffler has Lowry in his sights as the American moved into a share of fourth at two under despite dropping a shot at 18.
Scheffler has already won six times this year, including his second Masters title in April.
A monster putt at the 14th and a birdie on the par-five 16th took the American within striking range before a costly bogey on the last left him still five adrift of Lowry.
USPGA Championship winner Xander Schauffele is also well in the running at one under.
