Objective To assess pregnancy outcome in women who initially refused medically indicated caesarean delivery (CD) in cases of non-reassuring fetal heart rate (FHR) patterns. Study design A retrospective cohort study, comparing patients who refused and did not refuse caesarean delivery (CD) due to non-reassuring FHR tracings, was conducted. Deliveries occurred between the years 1988 and 2009 in a tertiary medical center. Multivariate analysis was performed to control for confounders. Results Out of 10,944 women who were advised to undergo CD due to non-reassuring FHR patterns, 203 women initially refused CD. Women refusing medical intervention tended to be older (30.6 ± 6.9 vs. 28.29 ± 6.1, P < 0.001) and of higher parity (46.8% vs. 19.9% had more than 5 deliveries; P < 0.001) as compared to the comparison group. Refusal of CD was significantly associated with adverse perinatal outcome. Using a multiple logistic regression model controlling for confounders such as maternal age, refusal of treatment was found as an independent risk factor for perinatal mortality (adjusted OR = 3.3, C.I. 95% 1.8–5.9, P < 0.001). A non-significant trend towards higher rates of adverse perinatal outcome was found when refusal latency time was longer than 20 min (OR = 2, 95% CI 0.36–11.95; P = 0.29). Conclusion Refusal of CD in cases of non-reassuring FHR tracings is an independent risk factor for perinatal mortality.