Transcranial magnetic stimulation (TMS) has been found to be promising in the neurorehabilitation of post-stroke patients. Aphasia and cognitive impairment (CI) are prevalent post-stroke; however, there is still a lack of consensus about the characteristics of interventions based on TMS and its neuropsychological and anatomical-functional benefits. Therefore, studies that contribute to creating TMS protocols for these neurological conditions are necessary. To analyze the evidence of the neuropsychological and anatomical-functional TMS effects in post-stroke patients with CI and aphasia and determine the characteristics of the most used TMS in research practice. The present study followed the PRISMA guidelines and included articles from PubMed, Scopus, Web of Science, ScienceDirect, and EMBASE databases, published between January 2010 and March 2023. In the 15 articles reviewed, it was found that attention, memory, executive function, language comprehension, naming, and verbal fluency (semantic and phonological) are the neuropsychological domains that improved post-TMS. Moreover, TMS in aphasia and post-stroke CI contribute to greater frontal activation (in the inferior frontal gyrus, pars triangularis, and opercularis). Temporoparietal effects were also found. The observed effects occur when TMS is implemented in repetitive modality, at a frequency of 1 Hz, in sessions of 30 min, and that last more than 2 weeks in duration. The use of TMS contributes to the neurorehabilitation process in post-stroke patients with CI and aphasia. However, it is still necessary to standardize future intervention protocols based on accurate TMS characteristics.