INTRODUCTION: World Health Organization estimates that the appropriate caesarean section rates should range from 10% to 15% at the population level. There is limited access and utilisation of caesarean section services in Uganda. This case-control study explored factors associated with caesarean section delivery, focusing on service-related and individual level factors. METHODS: we interviewed 134 cases that had a caesarean section and 134 controls that had a "normal" vaginal delivery. The study was conducted at health facilities in Kabarole district during March to May 2016. Multivariable logistic regression was used to determine individual factors associated with caesarean sections, at a significance level of p < 0.05. Key Informant (KI) data obtained from health workers was analysed using MAXQDA (version 12) software to determine health service factors affecting caesarean section service delivery. RESULTS: the mean age of the overall sample was 26 years (SD ± 6.5 years). Cases had 5% more women who belonged to the eldest age group (> 35 years) compared to the controls. The factors associated with caesarean section delivery were: having a previous caesarean section delivery (adjusted odds ratio (AOR): 4.5 CI: 2.22-9.0), attendance of four or more ANC visits (AOR: 2.0 CI: 1.04-3.83). Inadequate human resource, medicines and supplies affected access to the service. Misconceptions such as negative branding of women that have caesarean section deliveries as "lazy" reduced its acceptance thus low utilisation of the service. CONCLUSION: health system inadequacies and misconceptions about caesarean section delivery contributed to the low access and utilisation of the service.