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. The rehabilitation period for Tommy John surgery can be 12 to 18 months.
Fernandez, 21, was 4-2 with a 2.44 ERA in eight starts this season. He led the majors with 70 strikeouts.
However, he was roughed up during his last outing, last week against the San Diego Padres, giving up six runs in five innings, including two home runs.
Fernandez's fastball averaged 94.6 mph over his first four innings against the Padres but only 90.7 mph over his last two, according to ESPN's Stats & Information. He allowed four runs in the sixth inning before being removed with nobody out.
Last season Fernandez made 28 starts, going 12-6 with a major league-best .182 opponents' batting average. His 2.19 ERA was second in the majors behind three-time defending ERA champ Clayton Kershaw. Fernandez struck out 187 batters and was named NL Rookie of the Year.
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.
Information from The Associated Press was used in this report.