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Abstract Background There is substantial evidence that immunization is one of the most significant and cost-effective pillars of preventive and promotive health interventions. Effective childhood immunization coverage is thus essential in stemming persistent childhood illnesses. The third dose of pentavalent vaccine for children is an important indicator for assessing performance of the immunisation programme because it mirrors the completeness of a child’s immunisation schedule. Spatial access to an immunizing health facility, especially in sub-Sahara African (SSA) countries, is a significant determinant of Pentavalent 3 vaccination coverage, as the vaccine is mainly administered during routine immunisation schedules at health facilities. Rural areas and densely populated informal settlements are most affected by poor access to healthcare services. We therefore sought to determine vaccination coverage of Pentavalent 3, estimate the travel time to health facilities offering immunisation services, and explore its effect on immunisation coverage in one of the predominantly rural counties on the coast of Kenya. Methods We used longitudinal survey data from the health demographic surveillance system implemented in Kaloleni and Rabai Sub-counties in Kenya. To compute the geographical accessibility, we used coordinates of health facilities offering immunisation services, information on land cover, digital elevation models, and road networks of the study area. We then fitted a hierarchical Bayesian multivariable model to explore the effect of travel time on pentavalent vaccine coverage adjusting for confounding factors identified a priori. Results Overall coverage of pentavalent vaccine was at 77.3%. The median travel time to a health facility was 41 min (IQR = 18–65) and a total of 1266 (28.5%) children lived more than one-hour of travel-time to a health facility. Geographical access to health facilities significantly affected pentavalent vaccination coverage, with travel times of more than one hour being significantly associated with reduced odds of vaccination (AOR = 0.84 (95% CI 0.74 – 0.94). Conclusion Increased travel time significantly affects immunization in this rural community. Improving road networks, establishing new health centres and/or stepping up health outreach activities that include vaccinations in hard-to-reach areas within the county could improve immunisation coverage. These data may be useful in guiding the local department of health on appropriate location of planned immunization centres.