Introduction It is well known that emergency departments (EDs) suffer from crowding and throughput challenges, which make the ED a challenging workplace. However, the interplay between the throughput of patients and how staff experience work is seldom studied. The aim of this study was to investigate whether staff experience of work (efficiency, work-related efforts and rewards, and quantity and quality of work) differs between days with low and high patient throughput rates. Method Throughput times were collected from electronic medical records and staff (n = 252 individuals, mainly nurses) ratings in daily questionnaires over a total of six weeks. Days were grouped into low and high throughput rate days for the orthopedic, surgical and internal medicine sections, respectively, and staff ratings were compared. Results On days with low throughput rates, employees rated their efficiency, effort, reward and quantity of work significantly higher than on days with high throughput rates. There was no difference in perceived quality of work. Conclusions There is a complex relationship between ED throughput rates and staff perceptions of efficiency and efforts/rewards with work, suggesting that whereas low throughput may be troublesome from a patient and organizational perspective, working conditions may still be perceived as more favorable.