Pagan, an integral part of the Giants' World Series triumph last year, will undergo surgery today on his left hamstring.
Giants manager Bruce Bochy has said that Pagan's procedure, could keep the centre fielder and leadoff hitter on the sidelines for up to 12 weeks.
Such an absence would keep Pagan out until mid-September, shortly before the end of the MLB regular season. Rumours in the Giants camp suggest that if that is the case they are more likely to let him rest than risk a rushed return.
Pagan picked up the injury last week when undergoing rehabilitation for what was thought to be a minor issue. Instead of his condition improving, he aggravated his troubled hamstring and fell as he sprinted to first base.
The 31-year-old resisted surgery when it was cited as an option after he initially injured himself. The switch-hitter instead devoted his efforts towards healing himself enough to rejoin the lineup.
Having signed a four-year, $40m contract last offseason, Pagan hasn't played since May 25, when he hit a game-winning home run against Colorado.
Doctors will now attempt to repair the tendon on the inside edge behind Pagan's left knee.
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