Currently electroconvulsive therapy (ECT) is one of the only available therapies for treatment resistant depression (TRD). While effective, ECT is complicated by side effects, including cognitive impairment. One promising potential alternative is magnetic seizure therapy (MST). To date, no research has explored the effects of 100Hz MST on brain activity or the brain changes associated with response to treatment. Therefore the aim of this study was to determine the effects of a treatment course of 100Hz MST on regional brain glucose metabolism. Ten patients with treatment resistant depression underwent positron emission tomography with fluorodeoxyglucose before and after a treatment course of MST. Changes in the relative metabolic rate of a priori brain regions were investigated. Areas of increased relative metabolism after treatment were seen in the basal ganglia, orbitofrontal cortex, medial frontal cortex and dorsolateral prefrontal cortex. A secondary analysis showed trend-level differential findings in brain activation between responders and non-responders, namely in the ventral anterior cingulate. These results primarily indicate that MST is affecting regions consistent with the limbic-cortical dysregulation model of depression. Exploratory analysis indicated some differential findings in brain activation between responders and non-responders were also evident; however, the small sample size precludes any firm conclusions.