The coronavirus disease 2019 pandemic has significantly impacted the mental health of healthcare workers. This study aimed to assess the mental health of healthcare workers and identify risk and protective factors. We surveyed 48,031 healthcare workers at 63 Japanese Red Cross hospitals from December 15, 2022 to January 15, 2023. Mental health was assessed using the Center for Epidemiologic Studies Depression Scale, the Japanese Burnout Scale, and 10-item Connor-Davidson Resilience Scale. Furthermore, we inquired about the psychosocial support activities provided to the healthcare workers within their workplaces. This study included 3815 healthcare workers (250 doctors, 32 residents, 2588 nurses, 504 co-medical staff, and 441 administrative staff). Symptoms of depression were noted in 31.5% of all participants and 46.9% of resident doctors. Women and those who were young, lived alone, had a nonmanagement position, had contact with coronavirus disease 2019 patients, or had passive motivation to coronavirus disease 2019 work had a significantly higher total Center for Epidemiologic Studies Depression Scale score than in the corresponding groups with the opposite characteristics. High emotional exhaustion and depersonalization scores on the Japanese Burnout Scale were risk factors for depressive symptoms, while living with family was a protective factor. Moreover, interventions such as job performance support (skills, knowledge, information, and safety), peer support, and organizational support (infection control team, patient care rotation systems) were effective. The impact of the prolonged coronavirus pandemic on mental health among healthcare workers is clear, and organized psychosocial support is needed.