Interim Tiger coach Dabo Swinney said Harper's operation went well and he should return for Tuesday's practice.
The right-handed Harper had arthroscopic surgery on his throwing shoulder last fall.
Harper started the season as the favorite to win the Atlantic Coast Conference player of the year while the Tigers were expected to win the league title. However, he and the team have struggled and are 3-4.
Willy Korn, Clemson's starter in a 21-17 loss to Georgia Tech, sustained a bone bruise early in the game and is listed as questionable for the Boston College game. Clemson has next weekend off.