Neonatal jaundice is caused by high levels of unconjugated bilirubin. It is usually a temporary condition due to delayed induction of Ugt1a1, which conjugates bilirubin in the liver. To reduce bilirubin levels, affected babies are exposed to phototherapy (PT), which converts toxic bilirubin into water-soluble photoisomers, readily excreted out. However, in some cases uncontrolled hyperbilirubinemia leads to neurotoxicity. To study the mechanisms of bilirubin-induced neurological damage (BIND) in vivo we generated a mouse model lacking the Ugt1a1 protein and, consequently, mutant mice developed jaundice as early as 36 h after birth. The mutation was transferred into two genetic backgrounds (C57Bl/6 and FVB/NJ). We exposed mutant mice to PT for different periods and analyzed the resulting phenotypes from the molecular, histological and behavioral points of view. Severity of BIND was associated with the genetic background, with 50% survival of C57Bl/6-Ugt1(-/-) mutant mice at postnatal day 5 (P5) and at P11 for FVB/NJ-Ugt1(-/-) mice. Life-long exposure to PT prevented cerebellar architecture alterations and rescued neuronal damage in FVB/NJ-Ugt1(-/-) mice, but not in C57Bl/6 ones. Survival of FVB/NJ-Ugt1(-/-) mice was directly related to the extent of PT treatment. PT treatment of FVB/NJ-Ugt1(-/-) mice from P0 to P8 did not prevent bilirubin-induced reduction in dendritic arborization and spine density of Purkinje cells. Moreover, PT treatment from P8 to P20 did not rescue bilirubin-induced neurological damage accumulated up to P8. However, PT treatment administered in the time-window P0-P15 was sufficient to obtain full rescue of cerebellar damage and motor impairment in FVB/NJ-Ugt1(-/-) mice. The possibility to modulate the severity of the phenotype by PT makes the FVB/NJ-Ugt1(-/-) mice an excellent and versatile model to study bilirubin neurotoxicity, the role of modifier genes, alternative therapies and cerebellar development during high-bilirubin conditions.