Background Three-quarters of births in Indonesia occur in a health facility, yet the neonatal mortality rate remains high at 15 per 1000 live births. The Pathway to Survival (P-to-S) framework of steps needed to return sick neonates and young children to health focuses on caregiver recognition of and care-seeking for severe illness. In view of increased institutional delivery in Indonesia and other low and middle-income countries, a modified P-to-S is needed to assess the role of maternal complications in neonatal survival. Methods We conducted a retrospective cross-sectional verbal and social autopsy study of all neonatal deaths from June through December 2018, identified by a proven listing method in two districts of Java, Indonesia. We examined care-seeking for maternal complications, delivery place, and place and timing of neonatal illness onset and death. Results The fatal illnesses of 189/259 (73%) neonates began in their delivery facility (DF), 114/189 (60%) of whom died before discharge. Mothers whose neonate’s illness started at their delivery hospital and lower-level DF were more than six times (odds ratio (OR) = 6.5; 95% confidence interval (CI) = 3.4-12.5) and twice (OR = 2.0; 95% CI = 1.01-4.02) as likely to experience a maternal complication as those whose neonates fell fatally ill in the community, and illness started earlier (mean = 0.3 vs 3.6 days; P < 0.001) and death came sooner (3.5 vs 5.3 days; P = 0.06) to neonates whose illness started at any DF. Despite going to the same number of providers/facilities, women with a labour and delivery (L/D) complication who sought care from at least one other provider or facility on route to their DF took longer than those without a complication to reach their DF (median = 3.3 vs 1.3 hours; P = 0.01). Conclusions Neonates’ fatal illness onset in their DF was strongly associated with maternal complications. Mothers with a L/D complication experienced delays in reaching their DF, and nearly half the neonatal deaths occurred in association with a complication, suggesting that mothers with complications first seeking care at a hospital providing emergency maternal and neonatal care might have prevented some deaths. A modified P-to-S highlights the importance of rapid access to quality institutional delivery care in settings where many births occur in facilities and/or there is good care-seeking for L/D complications.