OBJECTIVE: The primary aim was to compare time from acute hamstring strain injury (HSI) to return-to-play (RTP) clearance following a standardized rehabilitation protocol performed within either pain-free or pain-threshold limits. Secondary aims were to compare isometric knee flexor strength, biceps femoris long head (BFLH) fascicle length, fear of movement, and reinjury occurrence at the 6-month follow-up between pain-free and pain-threshold groups. DESIGN: Randomized controlled trial. METHODS: Forty-three men with acute HSIs were randomly allocated to a pain-free (n = 22) or pain-threshold (n = 21) rehabilitation group. Days from HSI to RTP clearance, isometric knee flexor strength, BFLH fascicle length, fear of movement, and reinjury occurrence at the 6-month follow-up were reported. RESULTS: Median time from HSI to RTP clearance was 15 days (95% confidence interval [CI]: 13, 17) in the pain-free group and 17 days (95% CI: 11, 24) in the pain-threshold group, which was not significantly different (P = .37). Isometric knee flex or strength recovery at 90° of hip and 90° of knee flexion was greater in the pain-threshold group at RTP clearance by 15% (95% CI: 1%, 28%) and by 15% (95% CI: 1%, 29%) at 2-month follow-up, respectively. Improvement in BFLH fascicle length from baseline was 0.91 cm (95% CI: 0.34, 1.48) greater at 2-month follow-up in the pain-threshold group. Two reinjuries occurred in both the pain-free and pain-threshold groups between RTP clearance and the 6-month follow-up. CONCLUSION: Pain-threshold rehabilitation did not accelerate RTP clearance, but resulted in greater recovery of isometric knee flexor strength and better maintenance of BFLH fascicle length, compared to pain-free rehabilitation.