The central process of neonatal phototherapy by employing blue light has been attributed to the configurational conversion of (4Z,15Z)-bilirubin to (4Z,15E). Indeed, photoisomerization is the early photochemical event during this procedure. However, in this paper, we show that the bilirubin solutions under continuous blue light exposure undergo a photooxidation process. To ascertain the role of this photodegradation in the phototherapy, we evaluated UV–visible absorption spectra obtained from bilirubin solutions in CHCl3, milli-Q water, and physiological saline, as well as FTIR spectroscopy for bilirubin in CHCl3. These analyses also showed that the first 2 h of phototherapy are the most relevant period. In addition, quantum molecular modeling using B3LYP/6-31G(d,p) and ZINDO/S-CIS was performed to evaluate the electronic and structural properties of four bilirubin isomers, showing that the (4Z,15E)-bilirubin isomer is the most polar configuration. Therefore, it can be more soluble in aqueous environments than the other configurations. This clarifies why this is the faster isomer excreted during the phototherapy.