Background: Early functional mobilization (EFM) may improve patient outcome after Achilles tendon rupture (ATR). However, whether EFM affects patient outcome via changes in tendon elongation, thickening, or calf muscle atrophy is unknown. Purpose: To analyze differences in tendon and muscle morphology recovery over time between groups treated with EFM or standard treatment after ATR repair. Study Design: Cohort study; Level of evidence, 2. Methods: This prospective cohort study included 86 patients (20 women) with ATR repair who had a mean (SD) age of 39.3 (8.2) years and were part of a larger prospective randomized controlled trial. Patients were postoperatively randomized to immediate postoperative weightbearing and ankle motion (EFM group) or to immobilization in a below-knee plaster cast for 2 weeks (control group). Patient-reported and functional outcomes were assessed at 6 and 12 months with the Achilles Tendon Total Rupture Score and the heel-rise test for endurance. At 2 and 6 weeks and 6 and 12 months postoperatively, B-mode ultrasound imaging was performed to assess the length and cross-sectional area (CSA) of the Achilles tendon, the gastrocnemius CSA, as well as the thickness of soleus. Results: The Achilles Tendon Total Rupture Score for the EFM and control groups were 65.8 (18.7) and 56.8 (20.1; P = .045), respectively, at 6 months and 79.6 (15.8) and 78.9 (17.2; P = .87), respectively, at 12 months. At 2 weeks, tendon elongation was significantly more pronounced in the EFM group as compared with the control group (mean side-to-side difference, 1.88 cm vs 0.71 cm; P = .005). Subsequently, tendon elongation increased in the control group while it decreased in the EFM group so that at 6 and 12 months no significant differences between groups were found. Mean Achilles tendon elongation at 1 year was 1.73 (1.07) cm for the EFM group (n = 55) and 1.67 (0.92) cm for the control group (n = 27), with a mean difference of 0.06 cm (95% CI, 0.54 to –0.42; P = .80). Achilles tendon CSA and calf muscle atrophy displayed no significant differences between the groups; however, significant changes were demonstrated over time (P ≤ .001) in both groups. Conclusion: EFM results in more Achilles tendon elongation at early healing, but this difference subsides over time. EFM does not seem to affect patient outcome via changes in tendon elongation, thickening, or calf muscle atrophy. Registration: NCT02318472 (ClinicalTrials.gov identifier).