Burnout is common in emergency physicians. This syndrome may negatively affect patient care and alter work productivity. We seek to assess whether burnout of emergency physicians impacts waiting times in the emergency department. Prospective study in an academic ED. All patients who visited the main ED for a 4-month period in 2016 were included. Target waiting times are assigned by triage nurse to patients on arrival depending on their severity. The primary endpoint was an exceeded target waiting time for ED patients. All emergency physicians were surveyed by a psychologist to assess their level of burnout using the Maslach Burnout Inventory. We defined the level of burnout of the day in the ED as the mean burnout level of the physicians working that day (8:30 to the 8:30 the next day). A logistic regression model was performed to assess whether burnout level of the day was independently associated with prolonged waiting times, along with previously reported predictors. Target waiting time was exceeded in 7524 patients (59%). Twenty-six emergency physicians were surveyed. Median burnout score was 35 [Interquartile (24–49)]. A burnout level of the day higher than 35 was independently associated with an exceeded target waiting time (adjusted odds ratio 1.54, 95% confidence interval 1.39–1.70), together with previously reported predictors (i.e., day of the week, time of the day, trauma, age and daily census). Burnout of emergency physicians was independently associated with a prolonged waiting time for patients visiting the ED.