Thirteen months removed from arthroscopic surgery on the same right shoulder, Prior opted to have the problem taken care of this week, even if it meant having season-ending surgery to repair the tear in the anterior part of the shoulder capsule.
"After speaking with the doctors, Mark wanted to definitively fix it and begin the rehab process," said Prior's agent, John Boggs. "I think that's the best way to go about it."
Prior will undergo surgery this week in San Diego by team physicians Heinz Hoenecke and Jan Fronek. There's no timetable as to when Prior, who signed a one-year, $1 million deal in December, will return for one simple reason.
"Until you get in the area and see what is there, you don't know the extent of the injury," said Boggs, who noted that Prior will have an appointment Monday to determine the day of his surgery.
San Diego manager Bud Black first confirmed Prior's impending surgery before the start of Sunday's game against the Giants at AT&T Park.
"I can't imagine how frustrated he is," Black said. "He looked to be on his way back because the way he was throwing. It looked as though everything was on course. And then to have this happen ... I'm sure it's frustrating and disappointing. I'm sad for him."
Especially after the way Prior had progressed with his throwing program during the fall and winter. The Padres had initially given a soft target of May 1 as a day when he could possibly return to the Major Leagues, though that was made before Spring Training.
Prior, for the most part, progressed well during Spring Training and then into extended spring training after the Padres broke camp. He threw live batting practice to hitters in Arizona on April 2 but came down with tightness during the session.
"He was on track to make his progressions and then he ran into some difficulties," Black said. "He was still a ways away from passing the significant tests of game action. But leading up to that, just the way he was throwing, it lended itself to good things could happen."
San Diego general manager Kevin Towers said Sunday that "we were certainly hopeful he could come back. He was making progress. We felt the upside was worth the risk."
Prior, who is 42-29 with a 3.51 ERA in 106 career starts, last pitched for the Cubs in 2006, going 1-6 with a 7.21 ERA in nine starts. Prior was the No. 2 overall pick in the 2001 First-Year Player Draft out of USC and two years later was named to the National League All-Star team, the same season he went 18-6 with a 2.43 ERA.
Prior became a free agent in December, when the Cubs opted not to offer him a contract for 2008. There were anywhere from 11 to 14 teams interested in Prior, including the Houston Astros, who reportedly offered a larger base package. But Prior chose to sign with the Padres and stay in his native city.
Now he faces another uphill battle to get back to the Major Leagues. And while Boggs said his client is disappointed, he's still committed to completing his comeback.
"He's a guy who ever since I've known him, since he was at USC, is a battler," Boggs said. "I'm sure he was extremely frustrated. But he's committed to getting back on the mound and being a Major League starter."
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.