The COVID-19 pandemic that started at the end of 2019 forced populations around the world to reduce social and economic activities; it is believed that this can prevent the spread of the disease. In this paper, we report an analysis of the seismic noise during such an induced social activity reduction in the Tokyo metropolitan area, Japan. Using seismic data obtained from 18 stations in the Metropolitan Seismic Observation Network (MeSO-net), a two-step seismic noise reduction was observed during the timeline of COVID-19 in Tokyo. The first noise reduction occurred at the beginning of March 2020 in the frequency band of 20–40 Hz. This corresponded with the request by the Prime Minister of Japan for a nationwide shutdown of schools. Although social activity was not reduced significantly at this juncture, local reduction of seismic wave excitation in the high frequency band, 20–40 Hz, was recorded at some MeSO-net stations located in school properties. The second reduction of seismic noise occurred at the end of March to the beginning of April 2020 in a wider frequency band including lower frequency bands of 1–20 Hz. This timing corresponds to when the Governors of the Tokyo metropolitan area requested citizens to stay home and when the state of emergency was declared for the Tokyo metropolitan area by the government, respectively. Since then, the estimated population at train stations abruptly dropped, which suggests that social activity was severely reduced. Such large-scale changes in social activity affect the seismic noise level in low frequency bands. The seismic noise level started to increase from the middle of May correlating with increase in population at the train stations. This suggests that social activity restarted even before the state of emergency was lifted at the end of May. The two-step seismic noise reduction observed in this study has not been reported in other cities around the world. Unexpected reduction of social activity due to COVID-19 provided a rare opportunity to investigate the characteristics of seismic noise caused by human activities.