Background: Neonatal hyperbilirubinemia is a common condition requiring phototherapy, which, although effective, may lead to electrolyte disturbances. Objectives: To evaluate changes in serum electrolytes in term neonates undergoing phototherapy and to assess factors influencing these changes. Methods: This prospective observational study with a control group was conducted in a tertiary care hospital in Bikaner, Rajasthan. A total of 300 term neonates with hyperbilirubinemia were included, comprising 150 neonates receiving phototherapy (study group) and 150 neonates not requiring phototherapy (control group). Serum electrolytes (sodium, potassium, calcium, and magnesium) were measured at admission and after 48 hours. Data were analyzed using appropriate statistical tests, with p<0.05 considered significant. Results: Both groups were comparable in baseline characteristics. Serum bilirubin levels decreased significantly after phototherapy (p<0.001). A significant reduction in serum sodium, potassium, calcium, and magnesium levels was observed in the study group compared to controls (p<0.001). Hypocalcemia was the most common electrolyte abnormality (31.33%), followed by hyponatremia (16.66%), hypomagnesemia (14%), and hypokalemia (3.33%). The incidence of electrolyte disturbances increased significantly with the duration of phototherapy (p<0.001). Most neonates remained asymptomatic; however, hypocalcemia was the most frequent symptomatic abnormality. Conclusion: Phototherapy is associated with significant electrolyte disturbances in term neonates, particularly hypocalcemia. Routine monitoring of electrolytes, especially during prolonged phototherapy, is recommended to prevent complications.