Abstract Objectives This cross-sectional study aimed to examine the associations of a poor working environment at home with psychological distress and psychosomatic symptoms in employees working from home in Japan during the COVID-19 pandemic. Methods The data obtained in October 2021 from an online cohort of full-time employees (E- COCO- J) were used. Participants who worked from home for at least some days per month were included. The poor working environment at home was assessed using 11 items based on the Japanese Ministry of Health, Labour and Welfare recommended checklist. The score ranged from 0 to 11. Psychological distress and psychosomatic symptoms were measured by the Brief Job Stress Questionnaire (BJSQ). The associations between total scores of poor working environment and outcomes were examined by multiple regression analysis, adjusted by age, sex, education, living with family, frequencies of working from home, company size, job demand, job control, and workplace social support. Results Two hundred twenty-six employees who were working at home were included. The mean of the summed scores of poor working environments at home was 2.75. After adjusting the covariates, summed scores of poor working environments were significantly associated with high psychological distress (standardized β = 0.21, P = .003) and with high psychosomatic symptoms (β = 0.19, P = .005). For each poor environment, lack of ventilation and difficulty staying hydrated or resting were significantly associated with both outcomes. Conclusions Even after adjusting for job stressors and support, working environments at home were associated with employees’ mental health. Appropriate measures and education may be needed.