Backgrounds: Neonatal mortality rates in Indonesia remain steady in the past decades (20 in 2002 to 19 per 1000 live births in 2012). In order to accelerate the decline in neonatal mortality rate in Indonesia, specific interventions would have to target key factors causing mortality. This study aims to examine contribution of low birth weight on neonatal mortality in Indonesia. Methods: Data from the Indonesia Demographic and Health Survey (IDHS) conducted in 2012 were used in the analysis. A total of 18021 live births in the last five years preceding the survey were reported from the mothers. Completed information of their children (14837 children) were taken for this analysis. The adjusted relative risk with cox proportional hazard regression analysis were used to assess the strength of association to neonatal mortality. Results: Children born in low birth weight were 9.89-fold higher risk of neonatal mortality compared to children born in normal weight [adjusted relative risk (aRR) = 9.89; 95% confidence interval (CI): 7.41 – 13.19); P = < 0.0001]. Children delivered from younger mothers (aged 15 - 19 years) had 94% higher risk of neonatal mortality compared to children delivered from mothers aged 20-35 years. Working mothers had 81% higher risk of neonatal mortality compared to unemployed mothers. Conclusions: Children born in a low birth weight and born from younger mothers had higher risk of neonatal mortality. Appropriate care and treatment for children born in low birth weight is needed to prolonged survival rates of the children.