World number three McIlroy, who won at Dubai in January but hasn't taken a US PGA title this year, fired a two-under-par 70 to stand on six-under 210 after 54 holes at Muirfield Village in Dublin, Ohio.
David Lipsky (34), an American chasing his first PGA title, closed with back-to-back bogeys and fell into sharing the lead with McIlroy and South Korean Kim Si-Woo (27), who shot 71.
One stroke back on 211 were Norway's Viktor Hovland (25) and Americans Wyndham Clark (29), Mark Hubbard (34), Lee Hodges (27) and Denny McCarthy (30).
McIlroy, a 23-time PGA winner, had struggled after missing the cut at the Masters and sharing 47th at Quail Hollow, where he's a three-time champion.
But he shared seventh at the PGA Championship two weeks ago at Oak Hill despite feeling uncomfortable over the ball and has found better form with the US Open two weeks away.
"I'm feeling more comfortable than I felt at Oak Hill," McIlroy said. "I wouldn't say I'm 100%. But I'm battling and I'm hanging in there and the course is playing really tough.
"It feels better. I did a lot of real good work last week. I feel like I'm not fighting the club face as much as I have been so I'm able to release it a little bit more and have a little more trust in it.
"And with how tough it's playing this week, you need to trust it."
McIlroy blasted out of a greenside bunker and sank a 10-foot birdie putt at the par-five fourth, but made bogey at 10 after missing the fairway and taking four to find the green.
He answered with a birdie putt from just outside 25 feet at the par-three 12th then sank a six-foot birdie putt at the par-five 15th and answered a bogey at 16 with a seven-foot birdie putt at 17.
At 18, McIlroy knocked a 70-foot birdie putt almost nine feet past the hole but sank the comeback putt for par and pumped his right fist after booking his place in Sunday's final pairing with Kim and avoiding his first three-putt of the week.
"This course is still very playable from the fairways. I've done a good job of keeping the ball in play, hitting a lot of three-woods, a lot of irons off tees," McIlroy said.
"What I need to do tomorrow is just stick to that game plan, not try to get ahead of myself, not get too aggressive. If I stick to the game plan I've had for the last three days I'll be in with a great chance."
Kim feels 'great'
World number 38 Kim, who won his fourth PGA title in January at the Sony Open in Hawaii, made his second double bogey of the day at the par-5 11th then answered with birdies at 12, 13 and 15 to own a share of the lead.
"I feel great," said Kim, the 2017 Players Championship winner. "Making two doubles and shoot under par on this course, I'll take it."
Lipsky, ranked 160th, led much of the day and wasn't unhappy despite his poor finish.
"To find myself at the top of the leaderboard, I couldn't be happier," he said. "My short game has always been pretty good. I was able to lean on that today. I was able to hole a few nice par putts as well. Overall pretty happy."
Japan's Hideki Matsuyama (31), the 2021 Masters champion and 2014 Memorial winner, made three straight bogeys starting at eight and a triple-bogey at the par-3 12th on the way to a 75 to stand on 212.
American Justin Suh (25), the 36-hole leader, fired a 77 to finish on 213.
Reigning Masters champion Jon Rahm (28), the world number two from Spain, shot 74 to stand on 214. Top-ranked Scottie Scheffler (26) was on 215 after a 68.
