The neonatal period, or the first 28 days of life, is the most vulnerable time in a child’s life. Neonatal mortality has decreased in recent years. However, this progress varies at the national level, which necessitates actual regional data from different countries to identify local handicaps for life-saving precautions. This study aimed to investigate the causes for neonatal deaths as revealed by autopsy and histopathological examinations. A retrospective cross-sectional study was designed to identify the main causes of neonatal deaths in children who were autopsied at our institution between January 1, 2014, and December 31, 2021. Children who died within the first 28 days after birth (1–28 days of age) were referred to as neonatal cases. The main causes of neonatal death in children were determined via autopsy and histopathological and toxicological examinations. Furthermore, the causes of death were classified according to their manner of death. During this period, 122 neonatal children were autopsied at our institution. This group comprised 57 girls and 65 boys. For the manner of the death, natural causes were the most common cause (n = 91, 74.5%). Among natural causes, pneumonia (n = 66) was the leading one, representing 54% of all neonatal deaths, followed by perinatal conditions (n = 16, 13.1%). One of the pioneering reasons for death was sudden, unexpected postnatal collapse (n = 24, 19.6%), which was categorized under the undetermined group considering the manner of death. Unintentional (accidental) deaths accounted for 0.8% (n = 1) of total deaths, and intentional deaths were responsible for 6 neonates (4.9%) losses. This study shows that newborn children still die from simple and treatable infectious causes, probably arising from various familial and/or public inadequacies. In addition, sudden and unexpected postnatal collapse remains an important cause of neonatal mortality that has yet to be fully resolved. This study points out valuable inferences for caregivers and competent authorities to take preventive measures to prevent avoidable neonatal deaths.