Background User fee exemption for maternal and child health care service policy was introduced with a focus on providing free caesarean sections (CS) in Nigeria from 2011 to 2015. This policy had a positive impact on access to facility-based delivery, but its effect on socioeconomic and geographical inequality remains unclear. This study’s main objective is to examine access to birth by CS in the context of free maternal health care. Specifically, the study examines socio-demographic and geographical inequality in access to birth by CS among women who gave birth between 2011 and 2015 under the free maternal health care policy using a population-based survey data obtained from two of the six main regions of the country. Methods Data were obtained from 1227 women who gave birth during the period the policy was in operation selected using cluster random sampling between May and August 2016. Adjusted and unadjusted binary logistic regression models were used to examine whether there is socio-demographic and geographical inequality in access to birth by caesarean section. Results The overall caesarean section rate of 6.1% was found but varies by income (14.1% in monthly income of over $150 versus 4.9% in income of $150 and below), education (11.8% in women with higher education versus 3.9% among women with secondary education and less) and place of residence (7.8% in urban areas versus 3.6% in rural areas). Women who earn a monthly income of $150 or less were 48% less likely to have a birth by CS compared to those who earn more. Compared to women who were educated to tertiary level, women who had secondary education or less were 54% less likely to have birth by caesarean section. Conclusion This study shows that inequality in access to CS persists despite the implementation of free maternal health care services. Given the poor access to facilities with capabilities to offer CS in most rural areas, free maternal healthcare policy is not enough to make birth by CS universally accessible to all pregnant women in Nigeria.