For the second successive day, world number two McIlroy continued to be troubled by back spasms at East Lake but the defending FedEx Cup champion carded a 67, three better than his opening round.
He sits on 10 under overall despite telling Sky Sports “I’m limited”.
"I'm limited in what I can do, but I'm here grinding away, battling away," McIlroy was quoted on Sky Sports. "So happy to be through 36 holes.
"I felt like I had a little more speed. I was probably half a club off my numbers than maybe a full club yesterday. But still it's just hard to get my right side through the ball.
"It actually feels better with the longer clubs because I'm more upright in my posture. When I sort of get down to the shorter stuff, trying to stay in my posture is a struggle."
Norway's Viktor Hovland continued his recent scintillating form to surge into a share of the lead at the season-ending tournament.
The 25-year-old shot a course-record 61 to win the BMW Championship at Olympia Fields on Sunday.
Having opened with a two-under 68 at the Tour Championship, Hovland made the turn at one-under for his second round and the world number five found a flurry of birdies - five in six holes from the 12th - to card a 64.
That catapulted him into a share of the lead on 16 under, having started eight under due to the FedEx Cup's weighting system.
"I felt like a did a lot of the same stuff as yesterday...the front nine was decent but it was nice to get it going in the back nine," Hovland told Sky Sports. "We have all been grinding the whole year to be here and I'm in a great spot but we're only halfway there.”
Overnight leader Collin Morikawa, who posted his own round of 61 on Thursday, joined him with a birdie at the last to match his round of 64, with world number one Scottie Scheffler in third two shots behind after a 65. Jon Rahm, after a round of 65, is in a tie for fifth.