Purpose The hypothesis was that early functional mobilization would reduce the incidence of deep venous thrombosis (DVT) during leg immobilization after Achilles tendon rupture surgery. A secondary aim was to evaluate if the amount of weightbearing and daily steps influenced the risk of sustaining a DVT. Methods One-hundred and fifty patients with Achilles tendon rupture repair were randomized to treatment with early functional mobilization, encouraging full weightbearing and ankle motion in orthosis, or treatment-as-usual, i.e., 2 weeks of unloading in plaster cast followed by 4 weeks weightbearing in orthosis. At 2 and 6 weeks postoperatively, all patients were screened for DVT using compression duplex ultrasound. During the first 2 weeks postoperatively, patient-reported loading, pain and step counts were assessed. Results At 2 weeks, 28/96 (29%) of the patients in early functional mobilization group and 15/49 (31%) in the control group (n.s) had sustained a DVT. At 6 weeks, the DVT rate was 35/94 (37%) in the early functional mobilization and 14/49 (29%) in the control group (n.s). During the first postoperative week, the early functional mobilization group reported low loading and higher experience of pain vs. the control group (p = 0.001). Low patient-reported loading ≤ 50% (OR = 4.3; 95% CI 1.28-14.3) was found to be an independent risk factor for DVT, in addition to high BMI and higher age. Conclusions Early functional mobilization does not prevent the high incidence of DVT during leg immobilization in patients with Achilles tendon rupture as compared to treatment-as-usual. The low efficacy of early functional mobilization is mainly explained by postoperative pain and subsequent low weightbearing. To minimize the risk of DVT, patients should be encouraged to load at least 50% of body weight on the injured leg 1 week after surgery.