Background Neonatal jaundice is one of the most common conditions. Phototherapy has been accepted as the standard treatment for neonatal jaundice and the decline in the number of exchange transfusions in recent years is, at least in part, likely a direct reflection of the effectiveness of phototherapy at treating hyperbilirubinemia. However, this treatment modality also has some complications. One possible harmful consequence is potential immunotoxic effects by affection of lymphocytes subtypes which can affect the immune system functions in infants. Aim of the Work current study was performed to compare the effect of both conventional and tunnel phototherapy on lymphocytes subsets in term neonates (≥37weeks) with unconjugated hyperbilirubinemia. Patients and Methods The present study was conducted on 60 term neonates (≥37weeks) 40 of them with unconjugated hyperbilirubinemia admitted to NICUs in Ain-Shams University hospital during the period from January 2019 to July 2019. They were randomly assigned to 3 groups: 20 patients were exposed to conventional phototherapy and 20 patients were exposed to tunnel phototherapy and the other 20 healthy full term were assigned as control group. Total serum bilirubin (TSB), direct serum bilirubin (DSB), CBC, CD4 and CD8 percentages and absolute count were measured before and 48 h after phototherapy in the phototherapy groups. Baseline lab was done in the control group at once. Results significant decrease in total and direct bilirubin post-phototherapy in both phototherapy groups proved that tunnel phototherapy is as effective as conventional phototherapy as both provided rapid decrease in bilirubin levels. As regards the effect of phototherapy on lymphocytic count, we found that lymphocytic count significantly decreased post-phototherapy in both phototherapy groups. As regards the effect of phototherapy on CD4+ and CD8+ percentages, we found that CD4+ % significantly decreased postphototherapy in conventional phototherapy group. Moreover, when we measured CD4+ and CD8+ absolute counts, we found that CD4+ and CD8+ absolute counts significantly decreased post-phototherapy in both phototherapy groups. In the view of the effect of phototherapy on CD4/CD8 ratio, we found that the ratio significantly increased in tunnel phototherapy group. Conclusion Conventional and tunnel phototherapy which are used in the treatment of neonatal hyperbilirubinemia, affects the function of the immune system in newborns via alterations in CD4+ and CD8+ absolute counts.