The number of gastrointestinal cancer patients declined during the COVID-19 pandemic. In Japan, the number of early-stage gastric and colorectal cancer patients decreased significantly. However, how gastrointestinal cancers have changed with the shift to the “new normal” remains unknown. Herein, we compared the number of patients, stage at diagnosis, and detection process of the different gastrointestinal cancers in Japan across three periods: pre-COVID-19, Midst of COVID-19 pandemic, and during the transitional period to the “new normal”. The number of colorectal cancer patients decreased in the early phase of the COVID-19 pandemic. It then increased with the shift to the “new normal”, no longer differing from pre-COVID-19 levels. However, gastric cancer patients remained significantly fewer in the “new normal” period than in the pre-COVID-19 period, especially Stage I patients and patients detected through screening. Thus, people with undetected gastric cancer may not be receiving optimal screening, implying a negative prognostication for the near future.