Previous studies have reported that repetitive transcranial magnetic stimulation (rTMS) induces neuronal plasticity in the brain. Although event-related potential (ERP) is an exploration tool, the rTMS effects on ERPs in patients with major depression have not been fully explored. We demonstrated that rTMS treatment induces changes in brain function in patients with medication-resistant major depression using the ERP. Eighteen patients with medication-resistant major depression (five males and 13 females) participated in this study. The patients received rTMS treatment for 3 weeks. All patients completed clinical scales, including the Hamilton Depression Rating Scale (HAM-D), Hamilton Anxiety Scale (HAM-A), Beck Depression Inventory (BDI), State-Trait Anxiety Inventory (SAI, TAI), Ruminative Response Scale, Emotion Regulation Questionnaire, and Cognitive Emotion Regulation Questionnaire (CERQ), as well as the ERP auditory oddball task, at their first visit (baseline) and at the 3-week visit (3-weeks). The HAM-D, HAM-A, BDI, SAI, and “blaming others” scale of the CERQ decreased significantly after rTMS treatment. In ERP auditory oddball task, when FP1, FP2, FZ, FCZ, CZ, and PZ channels were analyzed, P200 amplitudes showed a main effect for time of measurement and increased after 3 weeks of rTMS treatment. Standardized low-resolution brain electromagnetic tomography showed significant activation in the left middle frontal gyrus by 3 weeks of rTMS treatment. The results suggest that relatively longer rTMS treatment induces changes in brain function in patients with medication-resistant major depression, which can be identified using ERP.