Objective: To compare the mean decrease in serum bilirubin after intermittent versus continuous phototherapy in the treatment of jaundice neonatorum. Methodology: This randomized controlled study was carried out on neonates admitted to the neonatal unit of Department of Paediatric Medicine, Ward A, Lady Reading Hospital, Peshawar from 1st October 2012 to 31st march 2013. A total of 258 patients were enrolled for the study after fulfilling the inclusion/ exclusion criteria to compare the decrease in serum bilirubin after applying continuous/intermittent phototherapy for the treatment of neonatal jaundice. Results: Mean age of the patients was 3.89±1.83(p=.91) days, the mean baseline bilirubin was 17.56mg/dl±1.42 (p=.36), while the mean follow-up bilirubin was 12.85mg/dl±1.65 (p=.95), and the mean difference between the baseline and follow-up bilirubin was 4.7mg/dl±1.19 (p=.32). For the group A babies, the mean difference between the baseline and follow-up bilirubin was 4.78mg/dl±1.20(p=.32). For the group B babies, the mean difference between the baseline and follow-up bilirubin was 4.63mg/dl±1.18(p=.32). The difference between the mean age on admission, mean baseline bilirubin, mean follow-up bilirubin, and the mean decrease in serum bilirubin for both the groups A and B was statistically not significant. Conclusion: Intermittent and continuous phototherapies were found to be equally effective. Because of its additional benefits intermittent phototherapy can be adopted as a routine procedure instead of continuous phototherapy in neonatal care unites.