Pineda, whom the Yanks obtained in an off-season trade with Seattle, has an anterior labral tear.
Dr. David Altchek, assisted by Yankees team physician Dr. Christopher Ahmad, will perform the anthroscopic procedure next week at the Hospital for Special Surgery in New York, MLB.com reported.
The 23-year-old right-hander has been on the disabled list since spring training with tendinitis in his throwing shoulder. He allowed 12 runs on 24 hits and 10 walks in 19 innings during the pre-season.
Pineda made the all-star team with the Mariners in his rookie season last year, when he went 9-10 with a 3.74 ERA in 28 starts.