Objective This study aimed to investigate the prospective effects of corporate and organizational workplace measures against COVID-19 on reducing employees' psychological distress during a 12-month follow-up in the COVID-19 pandemic. Methods Data were retrieved from an online longitudinal panel survey of full-time employees in Japan, with the 1st survey in March 2020, and the 2nd to 6th surveys in May, August, November 2020, February and March 2021, respectively. Seven area-specific workplace measures were assessed using a self-report 23-item scale at the 2nd follow-up. Psychological distress was measured using an 18-item scale of the Brief Job Stress Questionnaire at each survey. Linear regressions and mixed model analysis were conducted of psychological distress at follow-ups on scores of the area-specific workplace measures, adjusting for psychological distress and other covariates at the 1st survey. Results A total of 941 employees responded at baseline; most of them (86.9–90.9%) participated in the follow-up surveys. Linear regression analysis indicated that workplace measures of facilitating employees’ preventive measures (ie, hygiene behaviors) statistically significantly and negatively correlated with psychological distress at the 5th survey [b=-0.518, standard error (SE) 0.259, P=0.046]. A statistically significant and negative interaction between the scores and time of follow-up was observed in the mixed model analysis (b=-0.096, SE 0.047, P=0.041). No such correlation or interaction was found for any of other subcategorical workplace measures. Conclusions The study provides prospective evidence for a protective effect of workplace measures to facilitate employee’s hygiene behaviors on reducing psychological distress of full-time employees in the COVID-19 pandemic. The association seems stronger at a later follow-up.