Background: The Government of Indonesia is determined to follow global commitments to reduce the neonatal mortality rate. Yet, there is a paucity of information on contributing factors and causes of neonatal deaths, particularly at the sub-national level. This study describes careseeking during neonates' fatal illnesses and their causes of death. Methods: We conducted a cross-sectional community-based study to identify all neonatal deaths in Serang and Jember Districts, Indonesia. Follow-up interviews were conducted with the families of deceased neonates using an adapted verbal and social autopsy instrument. Cause of death was determined using the InSilicoVA algorithm. Results: The main causes of death of 259 neonates were prematurity (44%) and intrapartum-related events (IPRE)-mainly birth asphyxia (39%). About 83% and 74% of the 259 neonates were born and died at a health facility, respectively; 79% died within the first week after birth. Of 70 neonates whose fatal illness began at home, 59 (84%) sought care during the fatal illness. Forty-eight of those 59 neonates went to a formal care provider; 36 of those 48 neonates (75%) were moderately or severely ill when the family decided to seek care. One hundred fifteen of 189 neonates (61%) whose fatal illnesses began at health facilities were born at a hospital. Among those 115, only 24 (21%) left the hospital alive-of whom 16 (67%) were referred by the hospital. Conclusions: The high proportion of deaths due to prematurity and IPRE suggests the need for improved management of small and asphyxiated newborns. The moderate to severe condition of neonates at the time when care was sought from home highlights the importance of early illness recognition and appropriate management for sick neonates. Among deceased neonates whose fatal illness began at their delivery hospital, the high proportion of referrals may indicate issues with hospital capability, capacity, and/or cost.