BackgroundEarly Career Doctors (ECDs) in Nigeria are faced with many individual and systemic problems, which consequently adversely affect their health, well-being, patient care and safety.ObjectiveThis study, the second phase of the Challenges of Residency Training and Early Career Doctors in Nigeria (CHARTING II) Study, sought to examine the risk factors and contributors to the health, well-being and burnout amongst Nigerian ECDs.MethodsThis was a study of health, well-being and burnout amongst Nigerian ECDs. Outcome variables included burnout, depression, and anxiety, which were respectively assessed using the Copenhagen Burnout Inventory (CBI) and Oldenburg Burnout Inventory (OLBI), Patient Health Questionnaire (PHQ-9) depression scale, and Generalized Anxiety Disorder (GAD-7) scale. The quantitative data obtained was analysed using the IBM SPSS, version 24. Associations between categorical outcome and independent variables were assessed using chi square, with level of significance set at < 0.05.ResultsThe mean body mass index (BMI), durations of smoking and alcohol consumption of the ECDs were 25.64 ± 4.43 kg/m2(overweight range), 5.33 ± 5.65 years and 8.44 ± 6.43 years respectively. Less than a third (157, 26.9%) of the ECDs exercised regularly. The most common disease conditions affecting the ECDs were musculoskeletal (65/470, 13.8%) and cardiovascular diseases (39/548, 7.1%). Almost a third (192, 30.6%) of the ECDs reported experiencing anxiety. Male and lower cadre ECDs were more likely than female and higher cadre ECDs to report anxiety, burnout and depression.ConclusionThere is an urgent need to prioritize the health and well-being of Nigerian ECDs, so as to optimize patient care and improve Nigeria’s healthcare indices.