(1) To assess the efficacy of a specific rehabilitation protocol for femoroacetabular impingement syndrome (FAIS), patients who underwent hip arthroscopy (HA) were compared with a control group. (2) Patients with symptomatic FAIS who were scheduled for HA were randomized either to a control group (n = 45, 66.6% men, 41.8 ± 12.4 years) following a general post-surgical treatment protocol or to an experimental group (n = 45, 71.2% men, 40.9 ± 7.6 years) following a specific rehabilitation protocol supervised by a physiotherapist. Range of motion (ROM), orthopedic tests and pain were assessed immediately before surgery and at 4 and 14 weeks after surgery. The hip functional status was assessed by the modified Harris Hip Score (mHHS) before surgery and at the end of follow-up. (3) At 14 weeks after surgery and compared with the control group, the experimental group showed a lower percentage of positives for hip provocation tests (15.6% vs. 46.6% on Faber test; 15.6% vs. 77.8% on Fadir test; 2.2% vs. 20% on Ober test, experimental vs. control group, p < 0.001), a greater improvement in mHHS (27.2 vs. 10.7 points, p < 0.001) and higher ROM for all the movements evaluated: flexion (99.6 ± 12.2 vs. 89.6 ± 4.5, p < 0.001), extension (20.6 ± 5.8 vs. 13.3 ± 2.6, p < 0.001), adduction (30.6 ± 5.7 vs. 23.4 ± 8.4, p < 0.001), abduction (43.4 ± 10.7 vs. 32.8 ± 8.4, p < 0.001) and both internal (28.2 ± 8.5 vs. 18.7 ± 6.1, p < 0.001) and external hip rotation (36.8 ± 9.3 vs. 27.4 ± 5.6. p < 0.001). The pain decreased after surgery for both groups, although the reduction was greater in the experimental group at the end of intervention (13.8 ± 16.1 vs. 34.9 ± 16.3 mm, experimental vs. control group, p < 0.001). (4) The specific and supervised rehabilitation program in patients with FAIS undergoing HA showed better benefits at 14 weeks of treatment than the benefits achieved by a care protocol in terms of pain reduction and recovery of hip motion.