Introduction Vitamin D is important for its immunomodulatory role and there is an independent association between vitamin D deficiency and pneumonia. We assessed the effect of vitamin D supplementation on the outcome in children hospitalized for severe pneumonia. Methods This was a randomised, double blinded, placebo-controlled clinical trial in children aged >2–59 months with severe pneumonia attending Dhaka Hospital, icddr,b. Children received age-specific megadose of vitamin D₃ (20,000IU: <6 months, 50,000 IU: 6–12 months, 100,000 IU:13–59 months) or placebo on first day and 10,000 IU as maintenance dose for next 4 days or until discharge (if discharged earlier) along with standard therapy. This trial is registered at ClinicalTrials.gov, number NCT02185196. Findings We enrolled 100 children in placebo group and 97 in vitamin D group. On admission, 50 (52%) and 49 (49%) of children in vitamin D and placebo groups, respectively were vitamin D deficient. Among children with a sufficient serum vitamin D level on admission, a lower trend for duration of resolution of severe pneumonia in hours [72(IQR:44–96)vs. 88(IQR:48–132);p = 0.07] and duration of hospital stay in days [4(IQR:3–5)vs.5(IQR:4–7);P = 0.09] was observed in vitamin D group compared to placebo. No beneficial effect was observed in vitamin D deficient group or irrespective of vitamin D status. Conclusion Age-specific mega dose of vitamin D followed by a maintenance dose shown to have no statistical difference between the two intervention groups, however there was a trend of reduction of time to recovery from pneumonia and overall duration of hospital stay in under-five children with a sufficient serum vitamin D level on hospital admission.