Purpose: This study examined the effect of whey protein consumption following high-intensity interval swimming (HIIS) on muscle damage, inflammatory cytokines and performance in adolescent swimmers. Methods: Fifty-four swimmers (11–17 years-old) were stratified by age, sex and body mass to a whey protein (PRO), isoenergetic carbohydrate (CHO) or a water/placebo (H2O) group. Following baseline blood samples (06:00 h) and a standardised breakfast, participants performed a maximal 200 m swim, followed by HIIS. A total of two post-exercise boluses were consumed following HIIS and ~5 h post-baseline. Blood and 200 m performance measurements were repeated at 5 h, 8 h and 24 h from baseline. Muscle soreness was assessed at 24 h. Creatine kinase (CK), interleukin-6 (IL-6), interleukin-10 (IL-10) and tumor necrosis factor-alpha (TNF-α) were measured in plasma. Results: No difference in 200 m swim performance was observed between groups. CK activity was elevated at 5 h compared to baseline and 24 h and at 8 h compared to all other timepoints, with no differences between groups. Muscle soreness was lower in PRO compared to H2O (p = 0.04). Anti-inflammatory IL-10 increased at 8 h in PRO, while it decreased in CHO and H2O. Conclusions: Post-exercise consumption of whey protein appears to have no additional benefit on recovery indices following HIIS compared to isoenergetic amounts of carbohydrate in adolescent swimmers. However, it may assist with the acute-inflammatory response.