Primary somatosensory (SI) cortical inhibition to repetitive stimuli tends to decline with increasing age. However, aging effects on the inhibition mechanism of secondary somatosensory cortex (SII) remain elusive. We aimed to study the aging-related changes of cortical inhibition in the human somatosensory system. Neuromagnetic responses to paired-pulse electrical stimulation to the median nerve were recorded in 21 young and 20 elderly male adults. Paired-pulse suppression (PPS) of SI and SII activities was estimated by the ratio of the response to Stimulus 2 to the response to Stimulus 1. Based on equivalent current dipole modeling, PPS ratios of the contralateral (SIIc) and ipsilateral (SIIi) secondary somatosensory cortices were higher in elderly than in young subjects (p < 0.001 in SIIc and p = 0.034 in SIIi). At an individual basis, a higher PPS ratio in SIIc than in SI was found in 16 (80 %) out of the 20 elderly participants; in contrast, the PPS ratios of SIIc and SI cortices were similar in young participants (p = 0.031). In conclusion, a larger PPS ratio in elderly suggests an aging-related decline in somatosensory cortical inhibition. Furthermore, compared to SI, the electrophysiological responses of SII cortex are especially vulnerable to aging in terms of cortical inhibition to repetitive stimulation.