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The coronavirus disease 2019 (COVID-19) pandemic provides a unique opportunity studying individual differences in the trajectory of mental distress to relatively homogeneous stressors by longitudinally examining time-course changes between pandemic waves. For 21 months, we tested the effects of COVID-19 waves on mental health among 545 staffs at 18 hospitals treating COVID-19 patients in Shizuoka Prefecture, Japan. Contrary to increasing new infected cases as waves progressed, initially elevated psychological distress (K6) and fear of COVID-19 (FCV-19S) were decreased among waves (K6: B = -.02, 95% confidence interval [CI] = -.03 to -.01; FCV-19S: B = -.10, 95% CI = -.16 to -.04). This initial increase and subsequent decrease in K6 and FCV-19S were more prominent in individuals with high trait anxiety (K6: B = 1.55, 95% CI = 1.18 to 1.91; FCV-19S: B = 4.27, 95% CI = 2.50 to 6.04) and in occupations other than physicians or nurses. The current study revealed time-course changes in psychological distress and fear regarding COVID-19 in each pandemic wave and across waves, and indicated the usefulness of trait anxiety and occupation as predictors of mental health outcomes.