Objectives: Early detection of neonatal hearing impairment moderates the negative effects on speech and language development. Universal neonatal hearing screening protocols vary in tests used, timing of testing and the number of stages of screening. This study estimated the cost-effectiveness of various protocols in the preparation of implementation of neonatal hearing screening in Albania. Design: A micro-simulation model was developed using input on demography, natural history of neonatal hearing impairment, screening characteristics and treatment. Parameter values were derived from a review of the literature and expert opinion. We simulated multiple protocols using otoacoustic emissions (OAE) and automated auditory brainstem response (aABR), varying the test type, timing and number of stages. Cost-effectiveness was analyzed over a life-time horizon. Results: The two best protocols for well infants were OAE followed by aABR (i.e., two-stage OAE-aABR) testing in the maternity ward and single-aABR testing. Incremental cost-effectiveness ratios were €4181 and €78,077 per quality-adjusted life-year gained, respectively. Single-aABR screening led to more cases being detected compared to a two-stage screening program. However, it also resulted in higher referral rates, which increased the total costs of diagnostics. Multi-staged screening decreased referral rates but may increase the number of missed cases due to false-negative test results and nonattendance. Conclusions: Only the 2-stage OAE-aABR (maternity ward) protocol was below the willingness-to-pay threshold of €10,413 for Albania, as suggested by the World Health Organization, and was found to be cost-effective. This study is among the few to assess neonatal hearing screening programs over a life-time horizon and the first to predict the cost-effectiveness of multiple screening scenarios.