Indonesia's infant mortality rates are among the highest in South-East Asia, and there are substantial variations between its sub-national regions. This qualitative study aims to explore early mortality-related health service provision and gender inequity issues based on mothers' pregnancy, delivery and early-age survival experience in Ende district, Nusa Tenggara Timur province. Thirty-two mothers aged 18-45 years with at least one birth in the previous five years were interviewed in depth in May 2013. The results show most mothers have little knowledge about the danger signs for a child's illness. Mothers with early-age deaths generally did not know the cause of death. Very few mothers had received adequate information on maternal and child health during their antenatal and postnatal visits to the health facility. Some mothers expressed a preference for using a traditional birth attendant, because of their ready availability and the more extensive range of support services they provide, compared with local midwives. Unprofessional attitudes displayed by midwives were reported by several mothers. As elsewhere in Indonesia, the power of health decision-making lies with the husband. Policies aimed at elevating mothers' roles in health care decision-making are discussed as measures that would help to improve early-age survival outcomes. Widening the public health insurance distribution, especially among poorer mothers, and equalizing the geographical distribution of midwives and health facilities are recommended to tackle geographical inequities and to increase early-age survival in Ende district.