In 2006, Médecins sans Frontières (MSF) established an emergency obstetric and neonatal care (EmONC) referral facility linked to an ambulance referral system for the transfer of women with obstetric complications from peripheral maternity units in Kabezi district, rural Burundi. This study aimed to (i) describe the communication and ambulance service together with the cost; (ii) examine the association between referral times and maternal and early neonatal deaths; and (iii) assess the impact of the referral service on coverage of complicated obstetric cases and caesarean sections.