Transcranial magnetic stimulation (TMS) is a non-invasive modality of focal brain stimulation in which a fluctuating magnetic field induces electrical currents within the cortex. It remains unclear to what extent TMS alters EEG biomarkers and how EEG biomarkers may guide treatment of focal epilepsy. We present a case of a 48-year-old man with focal epilepsy, refractory to multiple medication trials, who experienced a dramatic reduction in seizures after targeting the area of seizure onset within the left parietal-occipital region with low-frequency repetitive TMS (rTMS). Prior to treatment, he experienced focal seizures that impacted cognition including apraxia at least 50-60 times daily. MRI of the brain showed a large focal cortical dysplasia with contrast enhancement involving the left occipital-parietal junction. Stimulation for 5 consecutive days was well-tolerated and associated with a day-by-day reduction in seizure frequency. In addition, he was monitored with continuous video EEG, which showed continued and progressive changes in spectral power (decreased broadband power and increased infraslow delta activity) and a gradual reduction in seizure frequency and duration. One month after initial treatment, 2-day ambulatory EEG demonstrated seizure-freedom and MRI showed resolution of focal contrast enhancement. He continues to receive 2-3 days of rTMS every 2-4 months. He was seizure-free for 6 months, and at last follow-up of 17 months was experiencing auras approximately every 2 weeks without progression to disabling seizures. This case demonstrates that rTMS can be a well-tolerated and effective means of controlling medication-refractory seizures, and that EEG biomarkers change gradually in a fashion in association with seizure frequency. TMS influences cortical excitability, is a promising non-invasive means of treating focal epilepsy, and has measurable electrophysiologic effects.