An MRI revealed that Pelfrey had a partial tear of the ulnar collateral ligament in his right elbow.
"It's frustrating," Pelfrey said. "I've never been hurt."
Pelfrey will visit with Dr. James Andrews on Friday, according to manager Terry Collins.
"The prognosis was not very good," Collins said.
"[The doctors] came back and said that I have a tear in my UCL and they brought up my options," said Pelfrey, who was placed on the disabled list on Tuesday with what was thought to be right elbow inflammation.
"They brought up the PRP, which is an injection. They put it at like 10-20 percent that it works, and so there was an 80 percent chance I was still gonna have surgery. So I thought it was the best case for me that we just go ahead and do it. Obviously, I'm still supposed to go down and visit Andrews personally and we'll go from there, but I think surgery is about 99 percent [that] it's gonna happen."
Pelfrey first began to experience "tightness" and "grabbing" on the first pitch of every inning in his last start on Saturday -- an eight-inning, one-run outing against the San Francisco Giants.
Initially, Pelfrey thought it was just standard tendinitis because he didn't feel any pain.
But after getting a precautionary MRI and a second opinion, it turned out to be much worse.
"I told them I can pitch, because I feel good," Pelfrey said. "But the thing that kind of backed me off was it was brought up to me that I could pitch and alter my mechanics and end up hurting my shoulder. And my shoulder feels great. And I think that's the last thing that I want."
This could mark the end of Pelfrey's career with the Mets. He's arbitration-eligible one more time but is making $5.6875 million this year, making him a definite non-tender candidate in December.
Pelfrey is the second-longest tenured Met behind third baseman David Wright. Pelfrey debuted in July 8, 2006.
Long term, the Mets could turn to highly touted Triple-A prospect Matt Harvey to possibly replace Pelfrey in the rotation. The flame-throwing 23-year-old is 2-1 with a 4.85 ERA in five starts for Buffalo.
The 28-year-old Pelfrey had pitched to a 2.29 ERA in his first three starts in 2012.
"I just feel terrible for you, especially right now with what you had to endure last summer, coming off a big year the year before, and right now pitching as good as I've seen you pitch in person," Collins told Pelfrey.
"He has his sinker back, he has command of his curveball. Everything was working. And to have this happen is a true shame, not only for him but for us."
Pelfrey owns a 50-54 record and a 4.36 ERA in 149 career starts, all for the Mets.
Mike Mazzeo is a regular contributor to ESPNNewYork.com.