McIlroy has a remarkable record in Abu Dhabi, with four second-place finishes, two thirds and a fifth in his last eight starts, but missed last year's event with the rib injury which disrupted his entire season.
The four-time major winner called an early end to his winless campaign, just the second of his professional career, in October, but reaped the rewards of some hard work over the winter with an opening three-under-par 69.
Playing partner and European number one Fleetwood carded a flawless 66 to lead by a shot from Paraguay's Fabrizio Zanotti, with the final member of the marquee group, world number one Dustin Johnson, struggling to a 72.
Starting from the 10th at Abu Dhabi Golf Club, McIlroy opened with 11 straight pars and could be forgiven for growing increasingly frustrated, especially after three-putting the par-five 18th for par.
However, the 28-year-old finally got into red figures by holing from 12 feet on the third and followed that with a tap-in birdie on the par-three seventh and another gain on the par-five eighth.
"I was excited to get going," McIlroy told Sky Sports. "The last couple of months have been really nice in terms of being able to concentrate on things I needed to work on in my game and health-wise. I feel like I'm nearly the most prepared for a season that I've ever been, but it was nice to get back out there and it was a great pairing to start off with.
"Tommy played very well and I was just trying to hang onto his coat-tails for most of the round, so really pleased; bogey-free 69 I can't really complain.
"I started off with 11 pars and it could have been a lot better than that so I tried to stay as patient as possible. When it's the first day back it's easier to stay patient so I was just trying my best and trying to hit a good shot every time I could, trying to hit good putts even if they weren't going in.
"I was proud of myself the way I hung in there. "
Fleetwood, whose victory 12 months ago set him on the way to winning the Race to Dubai, carded six birdies and hit all 18 greens in regulation, while Johnson mixed four birdies with four bogeys in an inconsistent display.
"[It was] very stress-free," Fleetwood said. "I played really well from start to finish and felt I did what you need to do round this golf course, which is drive it well. You can't be too greedy a lot of the time and my pace putting was really good.
"Just a really good ball-striking round and nice to start the year off like that."
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