Background: Neonatal morbidity and mortality is a global burden despite management measures that has been developed. Approximately 75% of all newborn deaths occur in the first week of life. In 2018 alone, around 2.5 million neonates died globally as a result of preventable causes such as prematurity, complications at birth, infections, and congenital abnormalities. Objective: The objective of the study was to determine neonatal morbidity and mortality patterns, and factors associated with mortality among neonates admitted in Wajir County Referral Hospital. Methodology: A hospital-based retrospective cross-sectional study was conducted among all neonates admitted to the New Born Unit of the WCRH from 01 January 2019 to 31 December 2020. A consecutive sampling technique based on the inclusion criteria was used. A data abstraction tool was used to extract data from the medical records of neonates admitted to the New Born Unit of the hospital. Results: A total of 615 neonates were included in the study. There were 336 (54.6%) male and 279 (45.4%) female neonates. Almost all the deliveries 566 (92.0%) were performed at the health facility with a minority of about 49 (8%) delivered at home. The home deliveries and referrals admissions from tertiary hospitals together were 66 (10.7%). Neonatal morbidity included birth asphyxia 335 (54.5%), neonatal sepsis 144 (23.4%), 57 (9.3%) meconium aspiration syndrome and 52 (8.5%) low birth weight/preterm. Overall mortality in 2019 at the health facility was 45 (12.97%) and in 2020, 35 (13.06%) presenting no significant difference. The deaths that occurred in the first 24 hours of life was 36 (45%). Bivariate and multivariate analysis produced a significant association between the factors associated with neonatal mortality. The multivariate analysis with day of admission (OR 2.872, 95% CI 1.293, 6.375), Sex, (OR 1.02, 95% CI 1.0.627, 1.66) and Birth weight, (OR 0.936, 95% CI 0.423, 2.068) at p<0.05. The logistic regression model was statistically significant, χ2(7) = 20.770, p <0.001. The model explained 27% (Nagelkerke R2) of the variance in discharge outcome and correctly classified 87% of cases. The male gender were 1.02 times more likely to die than females while the place of delivery was 0.572 times likely to result in death. Conclusions: Birth asphyxia was found to be the leading cause of admission, followed by neonatal sepsis and meconium aspiration syndrome respectively. The leading cause of death was birth asphyxia and neonatal sepsis. The mortality rate at the facility was 13%. Neonatal fatality of the newborns admitted to NBU is high in Wajir County. Since majority of the deaths are from preventable causes, this offers chances to improve newborn survival. Key Words: Morbidity, Mortality, Neonates, Asphyxia