Objectives Our study investigates the barriers perceived by staff in the referral systems in maternal healthcare facilities across Aceh province in Indonesia. Design With a cross-sectional approach, two sets of surveys were administered during September to October 2016 in 32 sampling units of our study. We also collected referral data in the form of the frequency of ingoing and outgoing referral cases per facility. Setting In three districts, Aceh Besar, Banda Aceh and Bireuen, a total of 32 facilities including hospitals, community health centres, and private midwife clinics that met the criteria of providing at least basic emergency obstetric and neonatal care (BEonC) were covered. Participants Across the 32 healthcare centres, 149 members of staff (mainly midwives) agreed to participate in our surveys. Primary and secondary outcome measures The first survey consisted of 65 items focusing on organisational measures as well as case numbers for example, patient counts, mortality rate and complications. The second survey with 68 items asked healthcare providers about a range of factors including attitudes towards the referral process in their facility and potential barriers to a well-functioning system in their district. Results Overall, mothers'/families' consent as well as the complex administration process were found to be the main barriers (36% and 12%, respectively). Healthcare providers noted that information about other facilities has the biggest room for improvement (37%) rather than transport, timely referral of mothers and babies, or the availability of referral facilities. Conclusions The largest barrier perceived by healthcare providers in our study was noted to be family consent and administrative burden. Moreover, lack of information about the referral system itself and other facilities seemed to be affecting healthcare providers and mothers/families alike and improvements perhaps through a shared information system is needed.