São Tomé and Príncipe (STP) uses a selective hepatitis B birth-dose vaccination (HepB-BD) strategy targeting infants born to mothers who test positive for hepatitis B virus (HBV) surface antigen. We conducted a field assessment and economic analysis of the HepB-BD strategy to provide evidence to guide development of cost-effective policies to prevent perinatal HBV transmission in STP. We interviewed national stakeholders and key informants to understand policies, knowledge, and practices related to HepB-BD, vaccine management, and data recording/reporting. Cost-effectiveness of the existing strategy was compared with an alternate approach of universal HepB-BD to all newborns using a decision analytic model. Incremental cost-effectiveness ratios (ICERs) were calculated in 2015 USD per HBV-associated death and per chronic HBV case prevented, from the STP health-care system perspective. We found that STP lacked national or facility-specific written policies and procedures related to HepB-BD. Timely HepB-BD to eligible newborns was considered a high priority, although timeliness of HepB-BD was not monitored. Compared with the existing selective vaccination strategy, universal HepB-BD would result in a 19% decrease in chronic HBV infections per year at overall cost savings of approximately 44% (savings of USD 5,441 each year). We estimate an ICER of USD 5,012 saved per HBV-associated death averted. The existing selective HepB-BD strategy in STP could be improved through documentation of policies, procedures, and timeliness of HepB-BD. Expansion to universal newborn HepB-BD without maternal screening is feasible and could result in cost savings if actual implementation costs and effectiveness fall within the ranges modeled.