Background Intern Medical Officers (IMOs) in Sri Lanka face significant challenges due to heavy patient load and scarcity of resources. Aims To assess IMOs' level of burnout, associated factors and the effects on self-reported patient care in comparison to postintern Relief House Officers (RHOs). Methods A descriptive cross-sectional study was conducted among IMOs and RHOs in two leading tertiary care hospitals in Sri Lanka. The level of burnout was assessed using Maslach Burnout Index. The self-reported health-related attitudes, practices, level of burnout, and their associations with patient care were compared between IMOs and RHOs. ResultsWe studied 114 participants (70 (61.4%) IMOs and 44 (38.6%) RHOs). IMOs were not involved in regular exercises (χ 2 (1) = 19.8, p = 0.000), skipped meals frequently (χ 2 (1) = 29.3, p = 0.000), and had a poor sleep quality (χ 2 (1) = 35.7, p = 0.000) compared to RHOs. Overall, 46.5%, 95.5%, and 86.7% of the participants were having moderate-to-high emotional exhaustion, depersonalization, and sense of poor personal achievement. The exhaustion and depersonalization levels were significantly higher among IMOs. Emotional exhaustion was significantly associated with poor sleep (U = 923.0, p = 0.014). Self-reported patient care negatively correlated with exhaustion (r s (112) = − 0.263, p = 0.005) and depersonalization (r s (112) = − 0.491, p = 0.000), while having positive attitudes correlated with better patient care (r s (112) = 0.208, p = 0.027). Conclusions The prevalence of burnout in IMOs in Sri Lanka is high, which, in turn, negatively correlates with patient care. IMOs face significant challenges in self-care, while their poor sleep perturbs daytime activities and conceivably interferes with patient care. Therefore, we recommend introduction of preventive measures to mitigate burnout in early-career physicians, particularly IMOs, to improve both self and patient care.