The surgery has been tentatively scheduled for July 6, and Smyly will miss the remainder of the season once the procedure is complete.
His expected timetable for recovery has been pegged between 12-15 months.
The announcement comes a day after Mariners pitching coach Mel Stottlemyre told reporters Smyly suffered a setback in his recovery that resulted in him getting scratched from a simulated start, according to the Seattle Times' Ryan Divish.
Smyly, 28, was initially diagnosed with a left flexor strain toward the end of spring training, and things spiraled out of control from there.
Now headed for a rehabilitation program that will span at least a year, Smyly will have to wait until next summer at the earliest to make his Mariners debut after the team acquired him in a January trade with the Tampa Bay Rays.
For his career, the southpaw is 31-27 with a 3.74 ERA, 1.199 WHIP and mark of 8.7 strikeouts per nine innings.