Introduction Emergency department (ED) crowding is a worldwide public health issue. In this study, patient flow and staff perceptions of crowding were assessed in Pakistan (Aga Khan University Hospital (AKUH)) and in the Netherlands (Haaglanden Medical Centre Westeinde (HMCW)). Bottlenecks affecting ED patient flow were identified. Methods First, a one-year review of patient visits was performed. Second, staff perceptions about ED crowding were collected using face-to-face interviews. Non-participant observation and document review were used to interpret the findings. Results At AKUH 58,839 (160 visits/day) and at HMCW 50,802 visits (140 visits/day) were registered. Length of stay (LOS) at AKUH was significantly longer than at HMCW (279 min (IQR 357) vs. 100 min (IQR 152)). There were major differences in patient acuities, admission and mortality rates, indicating a sicker population at AKUH. Respondents from both departments experienced hampered patient flow on a daily basis, and perceived similar causes for crowding: increased patients’ complexity, long treatment times, and poor availability of inpatient beds. Conclusion Despite differences in environment, demographics, and ED patient flow, respondents perceived similar bottlenecks in patient flow. Interventions should be tailored to specific ED and hospital needs. For both EDs, improving the outflow of boarded patients is essential.