Background and objective Integrating virtual reality (VR) and transcranial magnetic stimulation (TMS) offers a promising strategy for stroke rehabilitation, as it specifically focuses on reorganizing neural connections and activating brain activity in the cortex. The main goal is to create equitable connections between the brain's two hemispheres to enhance the execution of voluntary movements by stimulating the central executive network (CEN) to strengthen both motor and cognitive abilities. This study aims to propose a therapeutic approach that can improve cognitive recovery and overall quality of life in patients after a stroke. Methods A total of 69 participants were enrolled in the study based on certain inclusion and exclusion criteria. The patients underwent pre-assessment and wererandomly allocated into three groups: Group 1 received simultaneous repetitive TMS (rTMS)and virtual reality treatment (VRT), Group 2 received rTMS combined with sham VRT, and Group 3 received sham stimulation with VRT, in a 1:1:1 ratio using opaque, sealed, and stapled envelopes (SNOSE). Post-assessment was carried out using the same measures: the National Institutes of Health Stroke Scale (NIHSS), Addenbrooke's Cognitive Test (ACE III), and Montreal Cognitive Assessment (MOCA). Statistical analysis was conducted to determine the specific outcomes. Data analysis was carried out using IBM SPSS Statistics version 29 (IBM Corp., Armonk, NY), employing student's t-test for within-group comparisons and repeated measures ANOVA for between-group comparisons. The significance level was set at 5%. Results The results demonstrated statistical significance in NIHSS scores across all treatment groups (p<0.001). Regarding cognitive outcomes, improvements were observed in memory, language, and overall cognitive performance (ACE III) within all groups (p<0.05), with significant between-group outcomes (p = 0.009, p = 0.01, p = 0.004, respectively), suggesting variations in treatment effects across cognitive domains. However, no significant differences between groups were found in terms of fluency and visuospatial skills (p = 0.49, p = 0.13), indicating no treatment effects in these domains. Conclusions Based on our findings, the combined intervention involving rTMS and VRT, compared to sham treatments, demonstrates promising outcomes in alleviating stroke severity and improving specific cognitive functions such as memory, language, and overall cognitive performance. Additionally, the combined administrationoffers a more effective therapy than when they are administered separately.