Objective To investigate the effect of the coronavirus disease (COVID-19) pandemic on lifestyle behaviour and clinical data in a population who underwent an annual health check-up in Tokyo, Japan. Methods A self-report questionnaire was completed regarding changes in their physical activities, diet, alcohol intake, smoking and mental stress. For those recommended to undergo further examination or treatment, their intention to do so was also questioned. The clinical results of the check-ups across three different periods (before and during the pandemic and survey period) were statistically compared. Results During the survey period, 838 examinees responded. While physical activities decreased due to teleworking, changes in food intake and dietary patterns were varied. Furthermore, changes in mental stress were also diverse. As for the intention to undergo further clinical examination or treatment, 23.5% answered that they thought they would wait until the government lifted the state of emergency or the pandemic subsided. Compared with before the pandemic, diastolic blood pressure, liver function, kidney function and bone density tended to deteriorate. Conclusions The COVID-19 pandemic affected the lifestyle of the current study population. To prepare for future outbreaks, real-world information should be collected and shared so that effective measures for health promotion can be developed.