Sensory gating, a habituation-related but more basic protective mechanism against brain sensory overload, is altered in patients with migraine and linked to headache severity. This study investigated whether somatosensory (SI) gating responses determined 3-months treatment outcomes in patients with episodic migraine (EM) and chronic migraine (CM). A 306-channel magnetoencephalography (MEG) with paired-pulse stimulation paradigm was used to record their neuromagnetic responses. To calculate the peak amplitude and latency and compute the gating ratios (second vs. first amplitude), the first and second responses to the paired stimuli from the primary somatosensory cortex were obtained. All patients were assigned to subgroups labeled good or poor according to their headache frequency at baseline compared with at the third month of treatment. The gating ratio in the CM group (n = 37) was significantly different between those identified as good and poor (p = 0.009). In the EM group (n = 30), the latency in the second response differed by treatment outcomes (p = 0.007). In the receiver operating characteristic analysis, the areas under the curve for the CM and EM groups were 0.737 and 0.761, respectively. Somatosensory gating responses were associated with treatment outcomes in patients with migraine; future studies with large patient samples are warranted.