To examine the effect of the COVID-19 pandemic on the cardiovascular system in the general population, we compared ECG changes after the onset of the COVID-19 pandemic with those before the pandemic period. The incidence of newly appeared ECG abnormalities (T wave abnormalities, ST-segment depression including minor changes, and abnormal Q waves) from 2019 to 2020 (COVID-19 period) was compared with that from 2018 to 2019 (control period) in subjects 40 to 74 years of age without a history of cardiovascular disease who had 12-lead ECG recordings during annual health checkups offered to adult citizens of Moriguchi City, Osaka, Japan. Logistic regression analyses were performed after adjusting for cardiovascular risk factors. There were 5,221 eligible subjects in the control period and 4,100 eligible subjects in the COVID-19 period. The incidences of newly appeared ECG abnormalities were 5.2% for T wave abnormalities, 2.8% for ST-segment depression, and 1.1% for abnormal Q waves in the control period, whereas they were 5.8%, 4.3%, and 1.7% respectively, in the COVID-19 period. The incidence of ST-segment depression (odds ratio (OR) = 1.59, 95% confidence interval (CI) = 1.27-1.98, P < 0.0001) and that of abnormal Q waves (OR = 1.56, 95%CI = 1.09-2.22, P = 0.0149) in the COVID-19 period were significantly higher compared to those of the control period. In conclusion, increased incidences of newly appeared ST-segment depression and abnormal Q waves were observed during the COVID-19 pandemic period.