Newborn Screening (NBS) is a Philippine government program based on Republic Act 9288 for identification of neonates with genetic, metabolic, or infectious conditions, requiring provision of NBS to all newborns. Despite its passage, NBS provision is grossly underutilized in 2019. This study aims to identify factors influencing maternal utilization of NBS in two PhilHealth accredited Public tertiary hospitals in Quezon City. A sample of 399 mothers was obtained by multi-stage sampling. Logistic regression revealed that the factors that are associated with significant increase of maternal utilization of NBS were Hospital Offer (p < 0.001; OR = 25.629), PhilHealth membership (p = 0.049; OR = 1.677) and Hospital Location (p = 0.001,OR = 2.365) A direct offer of NBS to individual mothers increased maternal utilization of NBS the most; however, PhilHealth membership and hospital systems also played a large role in patient compliance. It is recommended that hospitals assign specific hospital staff to actively offer and be responsible for newborn screening prior to discharge, and that PhilHealth coverage is ensured for all.