PAWTUCKET — Jon Lester’s storybook comeback from the cancer ward to the major leagues hit a bit of a speed bump last night at McCoy Stadium, one he hopes is only a small one.

For the first time this spring, Lester did not dominate an opponent in his quest to recover from non-Hodgkins large-cell lymphoma. In fact, he struggled in three rocky innings against the free-swinging Indianapolis Indians last night at McCoy Stadium. The Indians went on to send the PawSox to their fifth straight loss, 5-1.

Lester, the left-hander the Boston Red Sox believe they’ll need in their starting five sometime this summer, surrendered two runs on three hits before being lifted after only three innings. He threw 63 pitches (39 strikes) on a night where the pre-game plans called for 90 throws or six innings, whichever came first.

Lester said he threw pain-free for two innings but felt some “mild cramping” in his left forearm in the third. When he reported the stiffness to Pawtucket manager Ron Johnson after the inning, the decision was made to call it a night.

“I hope it’s not a setback. It’s just a cramp,” Lester said. “My forearm tightened up a little bit. Hopefully it doesn’t set me back. Hopefully in five days I make another start and everything’s fine. I don’t know if it was dehydration or what. It was a little cramp in the forearm. They wanted to take me out. They didn’t want to take any risks with anything.”

Johnson said the decision was an easy one.

“It was my decision, mine alone,” he said. “We’re not going to send him back out there. It’s not a big deal. I don’t anticipate any problems.”

Lester was examined by the PawSox training staff and doctor Brian Busconi but no one seemed alarmed, least of all the 23-year-old who looked so impressive as a rookie last year in Boston when he went 7-2 in 15 starts. In late August his season ended when he was diagnosed with a treatable form of cancer. After a winter of treatment, he was cleared to begin playing baseball again this spring.

“I don’t see any reason for tests,” Lester said. “It’s in the forearm. There’s nothing to be worried about in the elbow or anything like that. It was just mild cramping.”

Before Lester tightened up, the Indians knocked him around a bit. He ran into quick trouble in the first inning. After striking out Nyjer Morgan to open the game, Lester walked Rajai Davis. Yurendell de Caster struck out on a sharp, 92-mph fastball for the second out, but Davis stole second base and advanced to third on a throwing error by catcher George Kottaras during de Casters’ at-bat. Chris Aguila then singled in Davis with a hard, bouncing shot past Lester into center field.

Jose Hernandez knocked in the second run of the inning when he hit a hanging cut fastball down the right-field line that bounced fair and rattled around the corner long enough for Aguila to race home from first base.

Lester settled down and retired the Indians in order in the second inning on just 12 pitches. The third inning didn’t go as smoothly. Lester gave up a leadoff single to Morgan, but he was erased by a Davis ground ball. The speedy Davis then stole second. On the next pitch, after Lester had stared him down a bit, Davis took off for third and was safe easily. Lester seemed shaken by the action on the bases and promptly walked both de Caster and Aguila to load the bases with one out.

Pitching coach Mike Griffin came out to talk to Lester and to his credit, the lefty settled down and battled his way out of the inning. First he struck out Hernandez on a sharp slider on the inside corner. Then he got Russ Johnson to ground into a force-out at short. He threw his fastball in the low-90s on the McCoy radar gun.

“I felt good,” Lester said. “Early on, I was throwing too many fastballs, which is what I usually try to do to get through the first inning. I just wasn’t quite there. It was probably going to be one of those nights that was going to be a battle, it was going to be a grind.”

Lester’s rehab assignment ends tomorrow and he’ll certainly be optioned to Pawtucket for more action. Whether it’s one, two or more starts is unclear, especially with Boston riding high in first place. Asked if he thinks he needs another start in Triple A, Lester quickly answered, “it wouldn’t hurt. But just like everyone else in that [PawSox] clubhouse, they don’t want to be here right now. They want to be in Boston. We’ll see what Theo [Epstein] and Tito [Francona] decide to do. I have to agree with that and go from there.”

kmcnamar@projo.com