Manager Mike Redmond announced Thursday the right-hander would have the elbow ligament transplant procedure. The decision was expected after the 21-year-old Fernandez was put on the disabled list this week.
''Our focus is to get him back,'' Redmond said before the Marlins began a four-game series in San Francisco. ''I'm glad he's having it done and starting his recovery process. Obviously it's a big blow for us.''
The operation will be done in Los Angeles. Fernandez becomes the latest in a string of major league pitchers this year who have needed Tommy John surgery.
Fernandez was 4-2 with a 2.44 ERA in eight starts this season.
Anthony DeSclafani, who started in place of Fernandez and made his major league debut during Sunday's 13-3 win over the Los Angeles Dodgers, will remain in the Marlins' rotation.