The four-time Major winner and two-time US PGA champion shot a four-over par 74, leaving him nine shots adrift of early clubhouse leader Jimmy Walker who filed a 65.
Amazingly, the Ulsterman completed his round without a birdie on the card, and he was as surprised as anyone.
"I know my game's there to give myself chances, just hopefully I'm not shut out tomorrow," he said. "I can't remember the last time I played a round without a birdie.
"I'll stay as patient as I can and try as hard as I can, and hopefully I can turn it around."
McIlroy played in one of the marquee groups alongside defending champion Jason Day and Open Championship runner-up Phil Mickelson. This was not the predicted outcome to McIlroy's bid for a third Wanamaker Trophy win.
The Baltusrol course sets up nicely for players who can drive the ball a long distance off the tee, and coming into the championship, McIlroy declared himself happy with his game.
He held to that view after the round in terms of tee-to-green performance, but 35 putts and not a single birdie undermined his scoring potential.
"There's just not a lot of momentum out there. But I'm happy with my game from tee-to-green," he said.
"I'm driving the ball as well as I have ever done. My iron play feels good. When I get on the greens, it's just a different story.
"I had a couple of chances early on that I could not convert and then missed a couple of greens and did not get up and down and I was always chasing it from there.
"I really struggled with the pace.
"They look much quicker than they are and two or three times I had putts within 12 feet that were downhill and left them short.
"I need to be more aggressive with my stroke, figure it out tomorrow and shoot something in the mid-60s and get into the weekend. That's the first objective. I will stay as patient as I can and try to turn it around."
This is McIlroy's second worst opening round score of the four Majors this year. He shot 70 at the Masters, 77 in the US Open and 69 at Troon in the Open. All of those were on par-72 layouts.
This par-70 at Baltusrol, featuring a plethora of long par-fours and long par-threes, with only two par-fives, ought to give up low scores, but enough players finished well over par yesterday to know that it demands respect. McIlroy can take heart from his 2012 performance.
That year he shot 75 in the second round of the US PGA at Kiawah Island, but went on to win.
"Look, it's one round of golf. I obviously want to play well, but I was trying my hardest out there," added the World No.4.
His compatriot, and Ryder Cup captain, Darren Clarke also shot a four-over 74.
Early clubhouse leader Walker said: "I feel like I've prepared and I'm ready to go this week. It's nice that that's what showed today.
"I felt like I was ready to go. Winning a Major would be huge but there's three days to go."
Walker is one shot ahead of Emiliano Grillo, Ross Fisher and Martin Kaymer.
Rickie Fowler is two under along with Jason Day.
Padraig Harrington is on one over along with Mickelson.
US PGA in numbers
4 - Phil Mickelson was four under par in winning the US PGA the last time it was staged at Baltusrol in 2005.
2011 - The last year in which all four majors were claimed by first-time winners (Charl Schwartzel, Rory McIlroy, Darren Clarke and Keegan Bradley). So far in 2016, Danny Willett (Masters), Dustin Johnson (US Open) and Henrik Stenson (Open) have won their maiden major titles.
28 - If world number one and defending champion Jason Day finishes lower than 28th, Johnson can replace him at the top of the rankings by finishing outright second or better.
347 - The length in yards of Byeong Hun An's winning effort in the long-drive contest held during Tuesday's practice round, just two yards further than long-time leader McIlroy.
1968 - The US PGA is being staged in July for the first time since 1968 due to the compressed schedule caused by golf's return to the Olympics.
17 - In 17 of the last 19 years, the champion has come from the last group in the final round.
19 - The number of rounds under par recorded by McIlroy since 2009, five more than nearest rival Steve Stricker.
6 - The world ranking of the last two major winners (Johnson and Stenson) at the time of their victories. Bubba Watson is the current number six.
3 - With victory this week, McIlroy would become the youngest player in history to have won three US PGA titles.
649 - The length in yards of the par-five 17th at Baltusrol.
Hole-by-hole guide to Baltusrol Golf Club
1st, 478 yards, par four: A challenging opener which plays as a par five for the members. Shunpike Road runs down the left-hand side and is out of bounds, while new bunkering has narrowed the landing zone. The green is relatively small by Baltusrol standards and surrounded by bunkers.
2nd, 378 yards, par four: Out of bounds again looms down the left and cross bunkers located 275 yards from the tee will force players to lay up short or take on the carry. The large green slopes sharply from right to left.
3rd, 503 yards, par four: A testing par four, although the hole bends to the left as it runs downhill to give extra distance to an accurate drive. Players finding the rough off the tee could be forced to lay up due to a creek which runs in front of a green divided by a ridge.
4th, 195 yards, par three: The first par three is protected by a pond in front of the green and was the site of a memorable occasion in 1952 when Robert Trent Jones was criticised for design changes which made the hole more difficult. Jones took some of his critics to play the hole and promptly recorded a hole-in-one. "Gentlemen, as you can see, the hole is eminently fair," he said.
5th, 424 yards, par four: The fairway is lined by bunkers but the approach to the green is crucial. Finding the putting surface is made difficult by a significant false front and a back left corner that feeds shots into a collection area.
6th, 482 yards, par four: A blind tee shot over a hogsback fairway but accurate drives will gain extra distance from the downslope. The approach is over flatter terrain into a large, well-bunkered and slightly undulating green.
7th, 505 yards, par four: The second hole on the front nine which plays as a par five for the members features the largest green on the course, but its kidney shape allows for tough pin positions tucked behind bunkers.
8th, 374 yards, par four: The shortest par four on the course offers a good birdie opportunity if the fairway bunkers can be avoided. The small green is surrounded by sand, with the most imposing bunker guarding the front.
9th, 211 yards, par three: Different tees can make a big difference to the angle of the approach to a narrow green which has an opening at the front but is otherwise guarded by bunkers.
10th, 464 yards, par four: Accuracy is vital off the tee as the fairway narrows to a bottleneck with a creek encroaching on the right-hand side. The green has a narrow opening in front that can kick balls in any direction.
11th, 444 yards, par four: A sharp dogleg left will see big hitters try to drive over the trees to cut the corner and set up a shorter approach to the most undulating green on the course.
12th, 220 yards, par three: The back of the green has been expanded to its original dimensions and a collection area added for shots which still go too far due to a putting surface which slopes from front to back.
13th, 462 yards, par four: A precise tee shot is required into a narrow landing area, with a creek crossing the fairway and running up the right hand side. Bobby Jones found the creek on his way to a shock defeat in the 1926 US Amateur but used the hole as inspiration when the 13th hole at Augusta National was designed.
14th, 430 yards, par four: The ideal drive carries the bunkers on the left of the fairway to set up an open view and shorter approach to the green. A safer drive to the right will leave a longer, partially blind approach.
15th, 459 yards, par four: A relatively straightforward hole which is framed by fairway bunkers and a green guarded by more sand. The green is large but has a subtle false front.
16th, 230 yards, par three: A downhill tee shot to a green surrounded by bunkers, where Lee Janzen chipped in for a vital birdie in the final round on his way to a two-shot win over Payne Stewart in the 1993 US Open.
17th, 650 yards, par five: Amazingly not even the longest par five in this year's majors - the 12th at Oakmont was 667 yards - the 17th unsurprisingly requires a long drive to allow players to carry the cross bunkers on their second shot. Anyone laying too far back will face an uphill, blind third shot to the green.
18th, 553 yards, par five: Almost 100 yards shorter than the 17th, the last is reachable in two as long as water to the left of the fairway and bunkers on the right can be avoided. In the 2005 US PGA Championship, Phil Mickelson came up just short of the green but got up and down for birdie to beat Thomas Bjorn and Steve Elkington by a shot.
Five possible winners at Baltusrol
1. Henrik Stenson
An obvious choice given his stunning victory in the Open, but Stenson would have been worthy of inclusion on the basis of his previous record in the event. Four of the 40-year-old Swede's top seven finishes in majors (before Troon) had come in the US PGA, including third places in 2013 and 2014. The only question is whether the world number five can carry the momentum from the Open with him across the Atlantic, or whether his heroics will catch up with him during a busy spell.
2. Phil Mickelson
Another easy option considering his 17-under-par total at Troon, including a major-equalling 63 in the first round and a flawless 65 on Sunday, would have won 140 of the 145 Open Championships ever staged. However, Mickelson also earns his place because of past performances, most notably his victory the last time Baltusrol staged the event in 2005. The 46-year-old left-hander has returned several times to use his status as an honorary member and has succeeded in getting his swing under control thanks to new coach Andrew Getson.
3. Zach Johnson
Finding players who did well at Baltusrol in 2005 and are still competing at the highest level is not easy, but two-time major winner Johnson (who finished 17th) fits the profile. Although he has not tasted victory since lifting the Claret Jug at St Andrews last year, Johnson has quietly been compiling a series of good finishes this season, including eighth in the US Open, 10th in the WGC-Bridgestone Invitational and 12th in the Open.
4. Dustin Johnson
US Open champion Johnson hit 71 per cent of fairways and 72 per cent of greens in regulation at Troon, but was undone by two costly double bogeys in round two and a triple bogey in the third. The world number two dropped five shots on the 11th hole alone and still finished inside the top 10 to continue his superbly consistent form in 2016. His power will also be a major advantage on the closing stretch which features a 230-yard par three and back-to-back par fives measuring 650 and 553 yards.
5. Patrick Reed
Made a flying start to the Open with an eagle and three birdies in the first seven holes before eventually signing for an opening 66. Being on the wrong side of the draw contributed to dropping out of contention with a second round of 74, but the Ryder Cup star battled back to finish in a tie for 12th to follow his share of 10th in the previous week's Scottish Open.