Pedroia, 34, returned to the lineup on May 26 but was back on the disabled list on June 2 with soreness in his knee. He is headed to Arizona to continue his rehabilitation treatment.
"I've healed quick with every other injury I've had. But this is obviously different," Pedroia told reporters Wednesday. "You can't risk it. If I come back too early and the graft fails, then that's it."
Earlier this week, Red Sox manager Alex Cora said he still expects the four-time All-Star to play again this season, but Pedroia said he'll know more "in 4 to 5 weeks" before making that determination.
"I'd love to play right now, but I can't," Pedroia said. "I'm going to be back for good if I let it heal. That's it. I've got to let it heal. ... I can't do anything about time."
Pedroia, who has played his entire career with the Red Sox, is signed with the team through 2021. Meanwhile, the Red Sox lead the AL East by 3.5 games over the New York Yankees.
"I love the way we're playing. I'm glad I got my one hit," Pedroia said. "I miss it, but I have to take care of this. ... I wish I could have a bigger part."