BACKGROUND This single-center study aimed to investigate the effects of repetitive transcranial magnetic stimulation (rTMS) on modulation of thyroid hormone levels and cognition in the recovery stage of patients with cognitive dysfunction following stroke. MATERIAL AND METHODS Seventy post-stroke patients who had cognitive impairment were randomly assigned to either the rTMS group or the control (sham) group. Both groups were administered basic treatment, with the rTMS group receiving rTMS (1 Hz, 90% MT, 1000 pulse/20 min, once a day for 5 days, for a total of 20 times), the stimulation site was the contralateral dorsolateral prefrontal cortex (DLPFC), and the sham group receiving sham stimulation which had the same stimulation parameters and site, except that the coil plane was placed perpendicular to the surface of the scalp. Cognitive function assessment and thyroid function tests were performed before and after 4 weeks of treatment. RESULTS Serum levels of triiodothyronine (T3), free triiodothyronine (FT3), and thyroid stimulating hormone (TSH) showed a positive correlation with Montreal Cognitive Assessment (MoCA) scale score of stroke patients in the recovery phase. The post-treatment change in the scores of MoCA and Modified Barthel Index (MBI) and scores of 3 cognitive domains (visuospatial function, memory, and attention), as well as serum T3, FT3, and TSH levels, were improved more significantly in the rTMS group, and T3 and FT3 levels significantly affected the MoCA scores within the reference range. CONCLUSIONS Serum T3, FT3, and TSH levels of stroke patients in the recovery phase were positively correlated with MoCA score. rTMS increased T3, FT3, and TSH levels and also improved MoCA and MBI of patients in the recovery phase of stroke.