Background: Death of a live-born baby within the first 28 days of life remains a critical global public health concern, particularly in low- and middle-income countries such as in sub-Saharan African, where refugee settlements often show higher varying neonatal mortality rates. This study aimed at assessing neonatal mortality rate and associated factors among neonates in Kiryandongo Refugee Settlement, Western Uganda. Subjects and Method: The study used a facility based retrospective cross-sectional design involving all neonates (0-28days) admitted over a 5-year study period at Panyadoli Hospital. A total of 510 records of neonatal admissions selected using systematic sampling. Logistic regression analysis was used to determine the factors associated with neonatal mortality and odds ratio was used as a measure of association. All statistical tests were two-tailed and p-value less than 0.05 were considered significant. Results: The neonatal death rate was 43 per 1,000 admissions. Neonatal mortality was significantly higher among mothers aged 25–34 years (aOR= 3.85; 95% CI= 1.74 to 8.90; p= 0.038) and ≥35 years (aOR= 7.88; 95% CI= 1.01 to 15.29; p= 0.049). It was also significant to those mothers delivering at home or in the community (aOR= 7.72; 95% CI= 2.04 to 31.45; p= 0.011), and those with pregnancy complications (aOR= 3.6; 95% CI= 1.93 to 8.14; p <0.001). Conversely, skilled birth attendance (aOR= 0.49; 95% CI= 0.21 to 0.69; p= 0.047) and an Apgar score of 4–6 at 1 minute (aOR= 0.12; 95% CI= 0.03 to 0.44; p= 0.002) were identified as protective factors. Conclusion: This study found a high neonatal mortality rate of 43 deaths per 1,000 admissions, highlighting the urgent need to strengthen antenatal, intrapartum, and postnatal/postpartum maternal and neonatal care to improve neonatal survival.