Background: Despite the global decline in neonatal mortality rates since ۱۹۹۰, reaching the Sustainable Development Goals (SDGs) targets by ۲۰۳۰ remains a considerable challenge. Three-quarters of infant deaths happen during the early infancy stage, influenced by fetal and maternal factors as well as health service readiness. Consequently, this period is crucial for mitigating the burden of infant mortality. Therefore, this critical period holds vital importance in alleviating the burden of infant mortality. Hence, the current study aimed to assess the factors contributing to early neonatal mortality, focusing on Afghan immigrant neonates and utilizing hospital information systems and medical records to identify potential determinants. Methods: Throughout a ۲۱-month study period from ۲۰۱۷ to ۲۰۱۸, data was collected from ۵۷۶ neonates, comprising ۴۴۱ neonatal near-miss (NNM) cases and ۱۳۵ neonates who died and were admitted to the neonatal intensive care unit across six selected hospitals. Data collection methods included thorough reviews of hospital systems and medical records and conducting telephone or face-to-face interviews using checklists and questionnaires. Statistical analysis was performed using SPSS version ۲۰ for Windows, with a significance level set at P<۰.۰۵ and confidence intervals at ۹۵%. A logistic regression model was employed for analysis, enabling control for confounding variables. Results about risk factors were presented as both unadjusted (crude odds ratio) and adjusted odds ratios (ORs) alongside corresponding ۹۵% confidence intervals (CIs). Statistical significance was established at a p-value of ≤ ۰.۰۵. Results: Our data demonstrated that age of ۲۰–۳۵ (AOR = ۱.۳۹۴, ۹۵% CI ۱.۲۰۹, ۳.۷۴۳; p = ۰.۰۰۵), mother's illiteracy [AOR ۲.۵۴۴, (۹۵% CI, ۱.۳۱۶–۶.۴۹۸; p = ۰.۰۳)], newborn insurance [AOR ۲.۵۴۴, (۹۵% CI, ۲.۳۸۷–۱۰.۶۵۶; p = ۰.۰۳)], risk factors of pregnancy [AOR ۱.۳۵۱, (۹۵% CI, ۱.۸۳۳–۵.۹۷۸; p = ۰.۰۰۳)], number of pregnancies ≥ ۵ [AOR ۳.۲۷۳, (۹۵% CI, ۲.۰۸۳–۱۰.۸۴; p = ۰.۰۰۲)], ۲-۴ pregnancies [AOR ۲.۵۳۹, (۹۵% CI,۲.۳۴۲–۶.۸۴۸; p = ۰.۰۰۷)], antenatal care [AOR ۵.۱۰۳, (۹۵% CI,۳.۱۷- ۰۵۶.۹۰۱; p = ۰.۰۰۱)], gestational age [AOR ۲.۳۸۵, (۹۵% CI, ۲.۳۲۲–۹.۶۵۲; p = ۰.۰۰۴)] and delay [AOR ۳.۱۷۸, (۹۵% CI, ۳.۰۸۴–۹.۳۷۶; p = ۰.۰۰۱)] were linked to an increased risk of neonatal mortality. According to our findings, the first delay (delay in decision-making for care) was the most important delay factor involved in neonatal death, followed by the third delay (delay in receiving services) and the second delay (access to services). Conclusion: The elevated neonatal mortality rate (NMR) observed among Afghan neonates in Iran underscores their heightened vulnerability when compared to their Iranian counterparts. Our study revealed significant associations between neonatal mortality risk and factors such as maternal age, maternal illiteracy, insurance coverage, pregnancy-related risk factors, high parity (≥ ۵ pregnancies), moderate parity (۲-۴ pregnancies), antenatal care, gestational age, and delays in care-seeking behaviors. These findings emphasize the imperative of implementing targeted interventions to support Afghan mothers and their neonates by enhancing access to comprehensive antenatal care, promoting health literacy, addressing maternal health complexities, and raising awareness about neonatal morbidity risk factors.