Background: Phototherapy is an effective and generally safe method of treating neonatal hyperbilirubinemia. However, there is some concern that it may affect cerebral blood flow velocity (CBFV) in newborns with fragile cerebral vasculature. Objectives: To measure and compare the effects of two different phototherapy units, delivering similar irradiance, on CBFVs. Methods: Doppler flow velocities were measured in term infants under fluorescent overhead and fluorescent BiliBed® phototherapy units, respectively, at baseline, 4 and 24 h of therapy. Results: Peak systolic CBFV increased during treatment in infants treated under overhead phototherapy (n = 18) but not in those treated in BiliBeds® (n = 12). Conclusions: Different phototherapy delivery modalities can have differential effects on CBFV in term neonates.