Repetitive transcranial magnetic stimulation (rTMS) with intensive occupational therapy improves upper limb motor paralysis and activities of daily living after stroke; however, the degree of improvement according to paralysis severity remains unverified. Target activities of daily living using upper limb functions can be established by predicting the amount of change after treatment for each paralysis severity level to further aid practice planning. We estimated post-treatment score changes for each severity level of motor paralysis (no, poor, limited, notable, and full), stratified according to Action Research Arm Test (ARAT) scores before combined rTMS and intensive occupational therapy. Motor paralysis severity was the fixed factor for the analysis of covariance; the delta (post-pre) of the scores was the dependent variable. Ordinal logistic regression analysis was used to compare changes in ARAT subscores according to paralysis severity before treatment. We implemented a longitudinal, prospective, interventional, uncontrolled, and multicenter cohort design and analyzed a dataset of 907 patients with stroke hemiplegia. The largest treatment-related changes were observed in the Limited recovery group for upper limb motor paralysis and the Full recovery group for quality-of-life activities using the paralyzed upper limb. These results will help predict treatment effects and determine exercises and goal movements for occupational therapy after rTMS.