Introduction: Pneumonia is the significant cause of morbidity and mortality in under five year children worldwide. In Nepal, pneumonia is the second most common cause of childhood mortality. Exclusive breastfeeding and basic immunization in preventing pneumonia cannot be underestimated. This study aims to assess the contributing risk factors associated with childhood pneumonia among children aged 16 months to under-5 year. Methods: A case-control study was conducted from January to July 2022 including children under 5 years visiting the pediatric out-patient department of JMCTH. A total of 200 subjects aged 16–59 months were enrolled, in which ‘cases’ included 100 patients diagnosed with pneumonia and ‘controls’ included 100 patients with non-pneumonia illnesses, matched by age and setting. The WHO guideline was followed for the diagnosis of pneumonia. The data on contributing risk factors were collected from both cases and controls via interview method from their parents. Results: The study showed non-exclusive breastfeeding [odds ratio (OR) =7.82 in 95% confidence interval (CI)], indoor air pollution [OR=7.47 in 95% CI], incomplete basic immunization [OR= 4.44 in 95% CI], low birth weight [OR=3.11 in 95% CI] and severe acute malnutrition i.e. high degree of wasting [OR=2.70 in 95% CI] were the major contributing factors of pneumonia in children under age five in the Madhesh Province of Nepal. However, nutritional status (height-for-age z score), age, sex, and educational status of mother did not appear to be contributing risk factors for pneumonia. Conclusion: This study highlights non-exclusive breastfeeding, indoor air pollution, incomplete basic immunizations, low birth weight, and severe acute malnutrition significantly increase the risk of childhood pneumonia. Exclusive breastfeeding plays a vital role, while gender seems to influence the relationship between exclusive breastfeeding and pneumonia incidence.