Introduction: Functional performance is impaired in patients with peripheral artery disease (PAD). The effects of a supervised exercise training (SET) program on functional performance have yet to be clearly determined. The aim was to investigate the time-course evolution of functional performance during a 3-month SET program. Methods: Patients with chronic symptomatic PAD participating in a 3-month SET program were investigated. Six-minute walking distance (6MWD), the stair climbing test (SCT), and the Short Physical Performance Battery (SPPB) were assessed before SET, after the first and second months of SET, and following the SET program. The ankle– and toe–brachial indices were measured before and after the SET program. Results: Ninety patients with PAD (age 65.4 ± 10.2 years) were analyzed. The 6MWD significantly improved after the first (+7%, p ⩽ 0.001) and second months (+13%, p ⩽ 0.001) and following SET (+14%, p ⩽ 0.001) compared to before the SET program. The 6MWD significantly improved after the 2nd month (+6%, p ⩽ 0.001) and following SET (+7%, p ⩽ 0.001) compared to after the first month of the SET program. The SPPB score and SCT performance significantly improved after the first (SPPB score: +9%, p ⩽ 0.001; SCT: +17%, p ⩽ 0.001) and second months (SPPB score: +11%, p ⩽ 0.001; SCT: +24%, p ⩽ 0.001) and following SET (SPPB score: +12%, p ⩽ 0.001; SCT: +25%, p ⩽ 0.001) compared to before the SET program. No significant differences were observed following SET compared to the second month of the SET program. Vascular parameters did not change significantly. Conclusions: A 3-month SET program improves several components of functional performance, and adaptations mainly occur during the 1st and 2nd months of the SET program.