Abstract Introduction: Childhood tuberculosis (TB) is one of the common causes of child mortality and morbidity in Bangladesh. The study aimed to assess the risk factors of extrapulmonary TB (EPTB) and pulmonary TB (PTB) in children and compare those with PTB amongst children. Materials and Methods: This hospital-based comparative study included EPTB and PTB cases ≤18 years. The groups were compared regarding various risk factors, including age, gender, socio-economic status, education level, nutritional status, family history, active and passive smoking, household contact, ventilation, overcrowding and contact duration. Results: Both EPTB and PTB patients were seen more in lower socio-economic groups (94%), and PTB was slightly higher (49% vs. 45% EPTB). Around 61% of EPTB cases occurred in the 11–18 age group, with a higher prevalence amongst females (61%) compared to males. Age was shown to have a significant association with EPTB, while the absence of ventilation, poor health status, overcrowding and contact duration displayed non-significant positive associations. The female gender, higher education, passive smoking and Bacillus Calmette–Guerin vaccination demonstrated statistically non-significant negative associations with EPTB in reference to PTB. Conclusion: It is essential to adequately address the risk factors to prevent children from both types of TB.