Maybin, who had an MRI on Monday, left Sunday's game after making a diving catch against the Los Angeles Dodgers. He played in only 14 games last season after suffering a torn posterior cruciate ligament in his left knee and having surgery on his right wrist.
"When he landed, it jarred the shoulder and did damage to the biceps tendon," Padres manager Bud Black told MLB.com.
Maybin, who was signed to a five-year extension worth $25 million prior to the 2012 season, has 70 stolen bases in two-plus seasons for the Padres, including a career-high 40 in 2011.
The Associated Press contributed to this report.