Objective: To investigate the influence of thrombolysis on functional outcomes after rehabilitation. Background: Systemic thrombolysis with tissue plasminogen activator (tPA) is considered the mainstay of acute stroke therapy and was found to improve short-term outcome. Design: Matched case-controlled design. Setting: Inpatient neurology and rehabilitation departments. Participants: Thirty-seven patients given tPA and 37 control patients not treated with lytics because of protocol limits. Methods: We retrospectively analyzed data from a cohort of stroke patients who were treated with systemic tPA. The rehabilitation outcome of thrombolysis-treated patients was compared with that observed for tPA-ineligible and age- and stroke severity-matched patients treated at the same neurology and rehabilitation departments. Main Outcome Measure: Neurological evaluation was assessed with the National Institutes of Health stroke scale (NIHSS). Activity of daily living was measured using the Functional Independence Measure (FIM) instrument. Functional outcome was measured using the modified Rankin scale (mRS). Results: The treatment group included 37 patients given tPA; 37 tPA-ineligible patients served as controls. On admission to rehabilitation, there were no significant differences in functional, neurological, and rehabilitation parameters between the groups. At the end of the rehabilitation period, NIHSS scores were significantly lower in the thrombolysis group (P = .036). More patients in the thrombolysis group reached functional independence defined as mRS ≤2 (20/37 versus 10/37; P = .03). At the end of rehabilitation, total FIM score (mean 102.8 versus 93.9; P = .039), total FIM gain (mean 27.8 versus 21.4; P = .09), and total FIM efficiency scores (0.8 versus 0.43; P = .013) were higher in the thrombolysis group and more patients in this group were discharged home. Conclusions: Although the bulk of neurological improvement occurred before the inpatient rehabilitation, thrombolysis-treated patients continue to improve faster and to a larger extent during the rehabilitation period suggesting that the beneficial effects of thrombolysis continue beyond the acute phase.