Aims:  In order for hospitals to work efficiently in a pandemic, it is important to know how a pandemic affects the hospital staff. The aim of the present study was to investigate the psychological impact of the pandemic (H1N1) 2009 on hospital workers and how it was affected by the characteristics of the hospital, gender, age, job and work environment. Methods:  In late June 2009, soon after the pandemic had ended in Kobe city, Japan, a questionnaire was distributed consisting of questions on sociodemographic characteristics, 19 stress‐related questions and the Impact of Event Scale (IES) to all 3635 employees at three core general hospitals in Kobe. Exploratory factor analysis was applied to the 19 stress‐related questions, and this produced four factors for evaluation (anxiety about infection, exhaustion, workload, and feeling of being protected). Multiple regression models were used to evaluate the association of personal characteristics with each score of the four factors and the IES. Results:  Valid answers were received from 1625 employees. Workers at a hospital with intense liaison psychiatric services felt less psychological impact. Workers at a hospital that provided staff with information about the pandemic less frequently, felt unprotected. Workers in work environments that had a high risk of infection felt more anxious and more exhausted. The total IES score was higher in workers in high‐risk work environments. Conclusions:  It is important for hospitals to protect hospital workers during a pandemic and to rapidly share information about the pandemic. Liaison psychiatric services can help to reduce the impact of the pandemic on hospital workers.