Repetitive transcranial magnetic stimulation (rTMS) is one of the non-invasive techniques, which is used to modulate cortical regions in patients with stroke. The aim of this single blind, controlled study was to investigate the effect of rTMS on swallowing function and quality of life of mono-hemispheric post-stroke patients with dysphagia. Twenty-eight patients were randomized and split between study and control group. Each group received conventional dysphagia rehabilitation 3 days a week for 4 weeks, and study group also received 1 Hz rTMS to unaffected hemisphere in the final week. The descriptive information was noted. The clinical and radiological swallowing evaluation and quality of life assessment have been performed at four different times including before and after the treatment, 1 month and 3 months after the treatment. At baseline, no significant differences were observed between groups in terms of demographic and clinical features (p > 0.05). Swallowing function and quality of life of the patients were statistically improved in both groups towards the third month (p < 0.05). Swallowing function was comparable between two groups. However, a significant improvement was observed on appetite, fear of eating, and mental health parameters of quality of life assessment in the study group compared to the control group (p < 0.05). In conclusion, despite positive changes in some aspects of quality of life, rTMS did not enhance the swallowing function when compared conventional dysphagia rehabilitation. Therefore, the application of 1 Hz rTMS should be reconsidered to improve swallowing function in the chronic period.