Background: Unlike the infant mortality rate, the rate of neonatal mortality has not declined and remains a major health challenge in low- and middle-income countries. There is an urgent need to focus on newborn care, especially during the first 24 hours of birth and the early neonatal period. Determining which factors contribute to neonatal near miss (NNM) can be used to assess health care quality and identify factors capable of correction in the healthcare system to improve neonatal care. Thus, the objective of the current study was to establish the prevalence of NNM and identify its associated factors.Methods: A hospital-based cross-sectional study was conducted at Koshi Hospital, Nepal. Neonates and their mothers (unspecified maternal age and number of gestational weeks) were enrolled. The key inclusion criterion was the admission of newborn infants to the neonatal intensive care unit at Koshi Hospital. Non-Nepali citizens were excluded. Consecutive sampling was used until the required sample size (i.e., 1,000 newborn infants) was reached. Simple and multiple logistic regression analysis was performed using SPSS ® version 24.0.Results: One thousand respondents were recruited. The prevalence of NNM was 79 per 1,000 live births. Maternal secondary (adjusted odds ratio (AOR]: 0.46, 95% confidence interval (CI]: 0.24–0.88) and tertiary education (AOR: 0.18, 95% CI: 0.05–0.56), multiparity (AOR: 0.52, 95% CI: 0.39–0.86), Caesarean section (AOR: 0.48, 95% CI: 0.19–0.99), and severe maternal morbidity (AOR: 4.51, 95% CI: 2.07–9.84) were significantly associated with NNM.Conclusions: Parity, severe maternal morbidity, mode of delivery, and maternal education were significantly associated with NNM. Healthcare workers should be aware of the impact of obstetric factors so that earlier interventions, especially the Caesarean section, can be exercised.