Objectives Neonatal deaths account for 45% of all under-five deaths globally and 60% in Bangladesh. This study aimed to investigate the most common symptoms and complications in neonates, care-seeking practices of the mothers for their sick neonates, and factors associated with the care-seeking practices. Methods This cross-sectional study analysed data from an Endline Household Survey (as part of an evaluation of a paired cluster-randomised controlled trial study in 14 rural sub-districts in Bangladesh) of 2,931 women who gave birth recently. Descriptive analysis and logistic regressions were conducted to identify the care-seeking practices of mothers of sick neonates and the factors associated with the care-seeking from trained providers. Results Of the 2868 neonates, 886 (30.9%) were reported ill during first 28 days after birth. For those with reported symptoms, 748 (84.4%) of their mothers sought care. Of those who sought care, 65.2% sought care from untrained providers. Multiple logistic regression analysis showed significantly higher odds of care-seeking from trained providers when neonates had 3 or more concurrent symptoms (OR: 1.82; 95% CI: 1.07±3.08); when mothers perceived their neonates' symptoms as severe (OR: 4.08; 95% CI: 2.92±5.70); when mothers received skilled care during pregnancy (OR: 1.95; 95% CI: 1.34±2.84); and when mothers had their delivery in a facility (OR: 3.50; 95% CI: 2.18±5.62). Mothers who delivered their babies at a facility, 43.1% of them sought care for their sick neonates at the same type of public hospital and 34.9% from same type of private hospitals where their deliveries took place. Conclusion Skilled care for mothers during pregnancy and delivery, and mothers' perceptions of the severity of symptoms are the key associated factors of care-seeking for sick neonates from trained providers. Interventions should be tailored to increase care from trained providers during pregnancy and delivery at facilities to improve care-seeking for neonates from trained providers and for the survival of neonates.