Background The Apgar score at five minutes is an important indicator of a neonate’s ability to survive and thrive. The association between Apgar score and adverse short-term outcomes in neonates (mortality, encephalopathy, and hospital stay) in Kenya remains unknown. Objectives To determine the distribution of Apgar scores in CIN hospitals and the association of Apgar scores with neonatal mortality, encephalopathy and hospital stay. Methods This retrospective cohort study was conducted in 22 neonatal units that are part of the Clinical Information Network(CIN) across 14 counties in Kenya. Singleton, inborn neonates admitted to the neonatal unit on day one of life between January 2018 and December 2022 were included. Results The study found that 77%, 20% and 3% of the 60,183 neonates had normal (≥7), intermediate (4-6) and low Apgar scores (≤3), respectively. The 5-minute Apgar score showed a statistically significant association with mortality; the adjusted hazard ratios of death among those with low and intermediate score 10.97 (95% CI: 9.45 – 12.73) and 3.60 (95% CI: 3.26 - 3.97), respectively, compared to those with normal. Compared with the normal Apgar score, the odds of developing encephalopathy were 5.73 (95% CI 5.37-6.12) and 15.87 (95% CI 13.9-17.6) times higher in the intermediate and low Apgar score categories, respectively. A low and intermediate Apgar score at five minutes was associated with a 25% (HR 0.75, 95% CI:0.63- 0.91) and 12% (HR 0.88, 95% CI:0.81- 0.95) lower risk of hospital discharge before 28 days, respectively, when compared to the normal Apgar score. Conclusion The five-minute Apgar score is an important determinant of adverse outcomes among neonates in primary referral facilities across Kenya. Correct assignment, use, and documentation of Apgar scores is necessary to improve the quality of neonatal care in primary referral facilities.