Obesity is a major public health challenge and results from the complex interaction of many etiopathogenetic factors. However, food-related hedonic stimuli and poor inhibitory control often appear to be specific maintenance factors, and conventional treatments are sometimes ineffective. Transcranial magnetic stimulation is emerging as a promising treatment option. Targeting specific brain regions, such as the dorsolateral prefrontal cortex, was found to be effective in modulating acute food craving and improving cognitive control. This review traces the evolution and development of transcranial magnetic stimulation and presents the results of recent randomized clinical trials conducted in obese subjects. These suggest that repetitive transcranial magnetic stimulation and deep transcranial magnetic stimulation may be effective in reducing body weight, BMI and food cravings. The neural circuits involved and the underlying mechanisms of action of this neurostimulation technique are also reviewed. Finally, outstanding questions and future research directions are identified to further understand and develop this promising therapy.