This methodological review identifies challenges in the development of health economic evaluations of newborn bloodspot screening (NBS) interventions and their consideration in NBS policy making. A systematic review of health economics methodological studies in NBS and stakeholder consultation was undertaken. The intervention under examination was defined as health economic decision analytic modelling used as decision support to NBS policy makers. An iterative search strategy was used to identify studies, and a data extraction framework was based upon a simple decision analytic model structure for the NBS decision problem. Synthesis was facilitated by two stakeholder workshops, which focused on ensuring the complete identification of challenges and developing recommendations. Sixteen methodological studies were identified. Data were extracted on challenges in decision criteria, decision variables, decision problem scope, defining model structure, selecting modelling method, the target condition, the screening test/protocol, outcome nodes, and other categories. Recommendations are made concerning supporting NBS decision making, NBS economic model structure and methods, data and estimation of model parameters, and overarching considerations. Recommendations for decision processes and methods research are put forward for the consideration of NBS policy makers and commissioners of research.