The Irishman rolled in a 20-footer as he followed his opening 66 with a two-under 69 on the Ayrshire coast.
“To shoot in the 60s is very good any day on this course, even when the conditions aren’t this bad. I’m very happy,” he told BBC Sport NI, referring to the 30mph winds that were buffeting the links during his round.
Lowry leads by two from England’s Dan Brown, the world number 272, who led overnight and backed up his sensational six-under-par opening round with a solid 72 on Friday.
World number one Scottie Scheffler, who has already won six times this year, including the Masters in April, hit a 70 to join fellow American Billy Horschel (68) and South African Dean Burmester (69) on two under.
Tiger Woods once again drew the biggest following of the morning starters and was afforded a huge ovation on the 18th as he closed with a six-over 77 that left him at 14 over.
There has been much speculation regarding the three-time Open champion’s future, given his lack of competitiveness after missing the cut at the past three majors, as he continues to recover from injuries sustained in a 2021 car crash.
However, when asked if he would be at Portrush for next year’s Championship, the 48-year-old replied: “Definitely.”
Woods’ playing partners Patrick Cantlay and Xander Schauffele will be here for the weekend. They are both at one under although Cantlay’s 68 was four shots better than his good friend could manage.
Scotland’s Robert MacIntyre, England’s Justin Rose and Northern Ireland’s Rory McIlroy are among the later starters.
‘He’s not happy’ – Lowry gets double bogey on eleventh
Lowry keeps head after Railway trouble
The 2019 champion birdied the first, fourth and eighth holes in relatively benign conditions as he reached seven under at the turn. But all his patient work threatened to unravel on the feared Railway.
The par-four 11th has been the toughest hole at the past three Troon Opens and Lowry found trouble off the tee with a slightly wayward drive into rough. From there he hit what former Solheim Cup captain Catriona Matthew called an “inexplicable hook” straight across the fairway and deep into a gorse bush.
He eventually stalked off the green with a double-bogey six and back where he started the day.
However, he steadied himself with four straight pars before closing with birdies on the 16th and 18th holes to set a target that may be tough to catch given the wind speeds are forecast to remain high.
“I faced a little bit of adversity in the middle of the round and I’m happy with how I dealt with it,” he told BBC Sport NI. “I moved on and hit some great shots coming in.
“I’ve got 24 hours until my tee time [on Saturday]. “I’m going to go home, chill out and soak it all in and then give it my best.”