Background For every newborn who dies within the first month after birth, as many as eight more suffer life-threatening complications but survive. Such events, termed ‘neonatal near-misses’, are becoming increasingly important indicators for epidemiologic surveillance and quality of care assessment. However, to date, there is no universally agreed-upon definition of a neonatal near-miss (NNM) nor a standard assessment mechanism. This study sought to describe the development of the Neonatal Near-Miss Assessment Tool (NNMAT) for low-resource settings, identify the incidence of NNM at three tertiary care hospitals in Ghana, compare the incidence rates of NNM to institutional records of neonatal mortality, and identify the strongest predictors of death when comparing NNM cases to those who died. Methods This prospective, observational, multi-center study was conducted at three tertiary care hospitals in southern Ghana from April – July 2015. Newborns with evidence of complications and those admitted to the NICUs were screened for inclusion using the NNMAT. Incidence of NNM was determined and compared against institutional neonatal mortality rates. NNM cases were compared with newborns not classified as near-misses and followed to 28 days to determine odds of survival. The main outcome measures were incidence of NNM, NNM:mortality ratio, and factors associated with NNM classification. Results Out of 735 newborns with complications, 578 (approximately 80%) were classified as near-misses using the NNMAT. Those newborns with complications who were classified as near-misses using the NNMAT had eight times the odds of dying before 28 days than those classified as non-near-misses. While most newborns qualified as NNM via intervention-based criteria, nearly two-thirds (approximately 65%) of newborns qualified based on two or more of the four NNMAT categories. When disaggregated, the most predictive elements of the NNMAT were gestational age < 33 weeks, presence of a major congenital abnormality, neurologic dysfunction and respiratory dysfunction. The ratio of near-misses to deaths was slightly less than 1:1, yet this varied widely across the three study sites. Conclusions This research suggests that the NNMAT is an effective tool for assessing neonatal near-misses in low-resource settings. We believe this approach has significant systems-level, continuous quality improvement, clinical and policy-level implications.