Padres manager Bud Black announced the decision to operate before Sunday's game against the San Francisco Giants. Prior, one of the top young pitchers in the game for the Chicago Cubs just a few years ago, has not pitched in the majors since Aug. 10, 2006.
He had been trying to make a comeback with his hometown Padres this season, but his rehab process was shut down at extended spring training about two weeks ago when he had more soreness in the shoulder. Prior, 27, had surgery on the same shoulder in April 2007 while with the Cubs.
"I can't imagine how frustrated he is," Black said. "It looked like everything was on course. Then to have this happen I'm sure is extremely frustrating. I'm upset for him just because there was such confidence from him about how he felt."
The operation to repair the anterior capsule in Prior's shoulder will be performed at Scripps Clinic as early as this week by team orthopedics Dr. Heinz Hoenecke and Dr. Jan Fronek.
The Padres won't know when, or if, Prior will be able to pitch again until after the operation.
"I think that will be determined once they go in and see what they have to repair," Black said.
Prior began throwing in January and was slowly making progress in hopes of a return to the majors. As recently as last month, the Padres still hoped Prior could make it back to the mound this season. But he never made it far enough to appear in a game at any level.
"You never know until you really step up the intensity," Black said. "And the fullest test of intensity is game action and he didn't get that far."
Prior, who is 42-29 with a 3.51 ERA in his injury-plagued career, last pitched in 2006 when he went 1-6 with a 7.21 ERA in nine games for the Cubs. He was the second overall pick in the 2001 amateur draft out of Southern California and went 18-6 with a 2.43 ERA in 2003, finishing third in NL Cy Young Award balloting in his first full season in the majors.
But he has made only 57 starts since 2003 because of injuries to his shoulder, elbow, oblique and Achilles.
Black also said that right-hander Cha Seung Baek will start Monday against the Cubs in place of injured lefty Shawn Estes, who broke the thumb on his pitching hand when he fell on the tunnel stairs between the team's clubhouse and dugout Friday in San Francisco.
Baek was acquired last week in a trade with Seattle. He struck out the side in the 12th inning to get the win in his Padres debut on Friday night against the Giants.