Bryce Harper missed the Phillies game with migraine but is expected to play Wednesday

NEW YORK — As if the Phillies weren’t having enough injury headaches, Bryce Harper came down with a migraine Tuesday.

The good news: It subsided before the end of a 4-0 win over the Mets.

“After a couple hours, he was good,” manager Rob Thomson said. “He’s had them before. He was ready to pinch hit if we needed it.”

Harper wasn’t at his locker after the game, but it’s expected that he will play Wednesday night when the Phillies and Mets shift their home-and-home series to Citizens Bank Park.

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The migraine came on about 20 minutes before the 1:10 p.m. first pitch, according to Thomson, who said it wasn’t related to a weird occurrence Monday night.

Harper was batting in the first inning of the series opener when he got grazed in the head by a stray throw back to the mound by Mets catcher Tomás Nido. Harper stayed in the game for the entirety of a come-from-behind, 5-4 victory in 10 innings.

“It had nothing to do with it,” Thomson said. “No.”

The Phillies already have Trea Turner on the injured list with a strained left hamstring. J.T. Realmuto has missed three games with a sore right knee.

Kyle Schwarber did return to the lineup, in his familiar leadoff spot, after not starting three consecutive games because of a stiff lower back. He went 1-for-3 with a double and two walks.

After scratching Harper at the last minute, the Phillies moved Alec Bohm to first base and inserted Whit Merrifield at third. Kody Clemens, in the original lineup at second base, stayed put, with Bryson Stott at shortstop.

“I said, ‘Just leave the middle guys [Clemens and Stott] there because they’ve already done their prep work,’” Thomson said. “Moved Bohm to first and put Whit at third and just made it simple. They all played well.”

Realmuto, who hasn’t played since Saturday in Miami, played catch and jogged on the field. Thomson is “hopeful” that Realmuto will be ready to play Wednesday night.

“Unless something weird happens overnight,” Thomson said, “and we’ll check him [Wednesday], but I expect him to play.”

In Realmuto’s absence, Garrett Stubbs started a third consecutive game behind the plate for the first time in his major-league career, making for easy comedy in the clubhouse.

“Stubby looks like he’s losing some weight,” Thomson joked about the popular but seldom-used backup catcher.

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Said Stubbs: “It was a lot of fun, man. I wish I could do it more. It is as fun as it gets also watching J.T. do his thing every single day, watching the best of the best. It makes me better, too. But it was fun catching three days in a row.”

Realmuto was available to catch in an emergency, Thomson said.

Neither the Phillies nor Realmuto believed there was a need to undergo diagnostic testing after his knee flared up while legging out a triple in the rain on May 4 at home. It didn’t bother him for a few days before the soreness returned last weekend in Miami.

Realmuto does play more than any catcher in the majors. He started 130 games in each of the last two seasons and started 34 of the first 39 games this season.

Will the Phillies have to scale back his workload when he returns?

“It all depends on how he feels,” Thomson said, “and sometimes you’ve got to take it away from him just to protect him.”

It was already shaping up as an eventful, if not straight-up bizarre, third inning Monday night when an athletic trainer visited the mound to take a look at Cristopher Sánchez’s left hand.

Sánchez felt what Thomson described as a “stinger,” a sensation that he has had before. It usually can be massaged away in a few seconds.

“No big deal,” Sánchez said through an interpreter. “With the treatment that they gave me right away, it’s not going to be an issue at all.”

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Sánchez began the third inning by throwing 24 pitches to four batters to load the bases and force in a run on a walk to J.D. Martinez. He struck out Brett Baty and Harrison Bader on a total of six pitches when his hand flared up.

After getting the issue cleared up, Sánchez notched another three-pitch strikeout of Jeff McNeil to complete the unusual inning. His secret: “I focused more,” he said after recovering to pitch into the sixth inning.

“That’s the growth in this guy,” Thomson said. “The biggest thing that I’m proud of him about is overcoming adversity. Long innings, the second and third, a lot of pitches put on him, and he just settled in and kept pitching.”

Rafael Marchán, the only other catcher on the 40-man roster besides Realmuto and Stubbs, was scheduled to begin a rehab assignment Tuesday night at low-A Clearwater. Marchán was sidelined by a back injury early in spring training. ... Clemens’ ninth-inning single Monday night against Mets closer Edwin Díaz marked the Phillies’ first pinch hit this season, snapping an 0-for-14 skid. Every other team in baseball had at least one pinch hit. ... Ranger Suárez (7-0, 1.50 ERA) is scheduled to start at home Wednesday night. The Mets haven’t named a starter.