The righty reliever has an injured UCL in his right elbow, which means there is a strong chance he will need Tommy John surgery.
Manager Bobby Valentine said the finding of Boston's medical staff was that Atchison had a torn UCL.
"Atch is getting another opinion," Valentine said.
A journeyman reliever for most of his career, Atchison became a force for Boston this season, going 2-1 with a 1.76 ERA in 37 games.
Atchison last pitched for the Red Sox on July 13. The club had hoped his injury was just a right forearm strain. But after opening his Minor League rehab assignment for Triple-A Pawtucket on Friday, Atchison not only was hit hard, but he didn't feel healthy.
That was the last time Atchison pitched. He underwent an MRI on Monday.
"As everyone knows, he had a little elbow soreness recently, we shut him down, we thought he was progressing pretty well, he went to make that rehab outing and felt it the next day really," said general manager Ben Cherington. "We had another MRI done, and it showed an injury to the UCL. He's going to get a second opinion, and we'll go from there."
With Atchison out of the mix and Matt Albers traded to the D-backs for lefty Craig Breslow, the Red Sox hope to get Daniel Bard back from Triple-A Pawtucket at some point in the near future.
"He's one of the guys that we know can help us and expect to help us," said Cherington. "There's no specific timetable on that."
Right-hander Andrew Bailey is also set to start a Minor League rehab assignment on Wednesday, so he should be a factor in two to three weeks.