Burnout syndrome is common among healthcare professions, including resident physicians. We aimed to assess the prevalence of burnout among resident physicians in Jordan, and a secondary aim was to evaluate the risk factors associated with the development of burnout syndrome in those residents, including gender, working hours, psychological distress, training sector, and specialty. In this cross-sectional study, 481 residents were recruited utilizing multistage stratified sampling to represent the four major health sectors in Jordan. Data were collected using an online questionnaire, where the Copenhagen Burnout Inventory (CBI) was used to assess the prevalence of burnout. The prevalence, group differences, and predictors of burnout were statistically analyzed using STATA 15. Overall, 373 (77.5%) residents were found to have burnout. Factors associated with higher levels of burnout were psychological stress (β = 2.34, CI = [1.88–2.81]), longer working hours (β = 4.07, CI = [0.52–7.62], for 51–75 h a week, β = 7.27, CI = [2.86–11.69], for 76–100 h a week and β = 7.27, CI = [0.06–14.49], for >100 h a week), and obstetrics/gynecology residents (β = 9.66, CI =[3.59–15.73]). Conversely, medical sub-specialty residents, as well as private and university hospital residents, had lower burnout levels. We concluded that decreasing the workload on residents, offering psychological counseling, and promoting a safety culture for residents might help in mitigating burnout consequences.