OBJECTIVES: The under-five mortality (U5M) rate in Kenya (41 per 1000 live births) remains significantly above international goals (25 per 1000 live births). This is further exacerbated by regional inequalities in mortality. We aimed to describe U5M in Migori County, Kenya, and identify associated factors that can serve as programming targets. DESIGN: Cross-sectional observational survey. SETTING: Areas served by the Lwala Community Alliance and control areas in Migori County, Kenya. PARTICIPANTS: This study included 15 199 children born to respondents during the 18 years preceding the survey. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was mortality in the first 5 years of life. The survey was powered to detect a 10% change in various health metrics over time with 80% power. RESULTS: A total of 15 199 children were included in the primary analyses, and 230 (1.5%) were deceased before the fifth birthday. The U5M rate from 2016 to 2021 was 32.2 per 1000 live births. Factors associated with U5M included year of birth (HR 0.926, p<0.001), female sex (HR 0.702, p=0.01), parental marriage (HR 0.642, p=0.036), multiple gestation pregnancy (HR 2.776, p<0.001), birth spacing less than 18 months (HR 1.894, p=0.005), indoor smoke exposure (HR 1.916, p=0.027) and previous familial contribution to the National Hospital Insurance Fund (HR 0.553, p=0.009). The most common cause of death was malaria. CONCLUSIONS: We describe factors associated with childhood mortality in a Kenyan community using survival analyses of complete birth histories. Mortality rates will serve as the baseline for future programme evaluation as a part of a 10-year study design. This provides both the hyperlocal information needed to improve programming and generalisable conclusions for other organisations working in similar environments.