Background: The neonatal mortality rate remains high in developing countries despite the significant reduction in under-five mortality globally. Therefore, periodic evaluations on the causes of mortality are an aspect of health status, which could be performed to improve the neonatal mortality rate. Objectives: The present study aimed to determine the pattern and causes of neonatal mortality in the Federal Medical Center in Owo, Ondo State, Southwest Nigeria. Methods: This retrospective study was conducted using the hospital records of the neonates admitted over a five-year period from 1st of January 2015 to 31st of December 2019. Results: In total, 2,065 neonates were admitted, including 208 cases of neonatal deaths. Mortality occurred in 127 males (61.1%) and 81 females (38.9%), with the male-to-female ratio of 1.6:1. Among the recorded deaths, 114 cases (54.8%) occurred within the first 24 hours of admission, while 94 neonates (45.2%) died after 24 hours of admission. In addition, the mortality rate was higher among outborn neonates (n = 120; 57.7%) compared to inborn neonates (n = 88; 42.3%). The major causes of neonatal deaths included birth asphyxia (46.6%), prematurity (23.1%), and sepsis (17.8%). The overall mortality rate over the five-year period was 10.1%, which is equivalent to 19 deaths per 1,000 live births. Conclusions: According to the results, preventable diseases such as birth asphyxia, prematurity, and sepsis remain the major causes of neonatal mortality, of which neonatal deaths occur mostly within 24 hours of admission.