Post-stroke upper limb spasticity is an important condition that negatively affects motor recovery, upper limb functions, and activities of daily living. Multimodal treatment approaches are recommended in the management of spasticity. In recent years, the effects of transcranial magnetic stimulation (TMS) on upper limb functions and spasticity have been investigated. However, the clinical effects of different TMS protocols combined with botulinum toxin-A (BTX-A) treatment and which protocol may be more effective remain unclear. The aim of this observational study is to compare the clinical effects of different TMS protocols in patients with post-stroke upper limb spasticity receiving BTX-A treatment and to evaluate the most appropriate TMS protocol.