San Diego manager Bud Black said Hermida will have sports hernia surgery that will sideline him for four to six weeks. The surgery will be performed by Dr. William Myers, who performed a similar surgery on Josh Hamilton of the Rangers last November.
"It just got too painful, and it wasn't going to go away," Black said on Monday.
The Padres completed a three-game series in Philadelphia on Sunday, and Hermida remained behind for a consultation and then subsequent surgery on Tuesday.
Hermida made the Opening Day roster in large part because Carlos Quentin had knee surgery on March 19 and started the season on the disabled list, as did Mark Kotsay because of a strained right calf injury he suffered at the end of Spring Training.
Hermida was hitting .250 with two RBIs in 27 plate appearances over 13 games. He went on the disabled list on April 28, retroactive to April 27.
San Diego catcher Nick Hundley had sports hernia surgery after the 2009 season and said the first few days after surgery were very painful.