Background: Stunting is a critical indicator of impaired growth among young children in Kenya, and understanding its risk factors is essential for designing sustainable interventions. This study aimed to assess the predictors of stunting among children aged 6–23 months in Kwale County, Kenya. Methods: An unmatched case-control study conducted from February to April 2022 involved 567 children aged 6-23 months, systematically sampled from the Kwale Health and Demographic Surveillance System (HDSS). Data were collected door-to-door using an electronic (ODK) structured questionnaire by trained enumerators. Data analysis was performed using Stata 17 for bivariate and multivariate logistic regression to identify predictors of stunting among the study participants. The variables with a p ≤ 0.2 were retained for a multivariable model, where a p<.05 was considered significant. Results: The independent predictors of stunting included: older age (13-23 months; AOR = 3.30, 95% CI:2.16-5.10), recent cough (AOR = 2.50, 95% CI:1.65-3.70), malaria (AOR = 2.20, 95% CI:1.32-3.63), caregiver employment (AOR = 2.30, 95% CI:1.43-3.63), household crowding (AOR = 1.80, 95% CI:1.16-2.83), residence in Kinango (AOR = 1.60, 95% CI:1.02-2.43), and low household wealth (AOR = 0.50, 95% CI: 0.26-0.98). Low birth weight showed a borderline association (AOR = 1.90, 95% CI:1.00-3.50). Conclusion: Stunting remains highly prevalent in Kwale County, driven by child-level, household, and environmental factors. A multisectoral response targeting WASH, housing, and social support could reduce stunting risk. Additionally, educating caregivers on these risks is crucial to raise awareness and mitigate long-term impacts.