Background: Medical practice and education are known to lead to emotional and mental exhaustion as well as physical tiredness among healthcare workers. This study analyzed the prevalence and factors associated with physician burnout syndrome (PBS) among resident doctors in paediatric across Nigeria. Methodology: This cross-sectional study was conducted among paediatric resident doctors across Nigeria using the public welfare questionnaire of the American Welfare Association comprising 28 questions related to sleep affectation, energy levels, personal relationships, professional relationships, quality of job environment, and work satisfaction. Results: 117 residents were enrolled with varying degrees of burnout. The mean PBS score was 75.3 ± 19.1 with minimum and maximum scores of 32 and 125, respectively. The prevalence of Grades 0, 1, 2, 3, and 4 PBSs was 3.7%, 4.9%, 28.1%, 42.7%, and 18.3%, respectively, while 63.4% of respondents exhibited signs of symptomatic PBS. The residents' rank (P = 0.05) was significantly associated with the prevalence of symptomatic PBS, while age (P = 0.567), gender (P = 0.755), number of years in training (P = 0.411), marital status (P = 0.173), number of children (P = 0.974), religion (P = 0.09), and prior knowledge of PBS (P = 0.719) had no association with the development of symptomatic PBS among surveyed resident doctors. Conclusion: The prevalence of PBS is high among paediatric resident doctors. There is an urgent need for the postgraduate medical colleges in collaboration with the Ministry of Health to formulate programmes that will help to balance social and professional lives among paediatric resident doctors in Nigeria.