PHILADELPHIA — Aaron Boone said Will Warren wouldn’t be “overwhelmed” in his MLB debut Tuesday, filling in for Gerrit Cole — who was scratched with body fatigue.

The first time through the Phillies’ batting order, though, Warren sure seemed overwhelmed.

There was a leadoff walk to Kyle Schwarber and an RBI double from Alec Bohm later in the first.

And in the second, the right-hander gave up a single to J.T. Realmuto, a lineout to Nick Castellanos and a walk to Bryson Stott before Austin Hays took him deep for a three-run homer.

But Warren recovered and retired 12 of the next 14 batters he faced before being removed with one out in the sixth and the Yankees trailing by two runs.

He ended up giving up four runs in 5 ¹/₃ innings in the Yankees’ 7-6, 12-inning win at Citizens Bank Park.

A Jazz Chisholm Jr. three-run homer took Warren off the hook for the loss, as it gave the Yankees a one-run lead — which Clay Holmes blew in the bottom of the ninth.

It’s been an interesting path to the majors for the 25-year-old Warren this season.

He was in the mix to take Cole’s spot in the rotation during spring training before Luis Gil won the job.

Warren then went out and put up an 8.53 ERA in his first 10 starts at Triple-A Scranton/Wilkes-Barre.

Warren — ranked as the second-best Yankees pitching prospect by MLB Pipeline, behind Chase Hampton — has risen in the rankings in part due to the Yankees having sacrificed a lot of young pitchers in recent trades.

He’d pitched better of late and got good results in three of his final four starts at Triple-A before getting called up Tuesday.

“He’s a confident kid,’’ Boone said before the game. “We love his makeup, love his stuff. He’s had some bumps in the road this year [at Triple-A], but he also dominated a lot of outings. He has all the equipment to go out there and be successful.”

Pitching coach Matt Blake said the team was impressed with Warren’s demeanor and the fact he recovered after his rough stretch in the minors.

“He weathered his struggles early and made adjustments,’’ Blake said. “We feel like he’s gonna be all right in this environment.”