Background With a view to improve neonatal survival, data on birth outcomes are critical for planning maternal and child health care services. We present information on neonatal survival from Ifakara Health and Demographic Surveillance System (HDSS) in Tanzania, regarding the influence of mother’s age and other related factors on neonatal survival of first and second births. Methods The study conducted analysis using longitudinal health and demographic data collected from Ifakara HDSS in parts of Kilombero and Ulanga districts in Morogoro region. The analysis included first and second live births that occurred within six years (2004–2009) and the unit of observation was a live birth. A logistic regression model was used to assess the influence of socio-demographic factors on neonates’ survival. Results A total of 18,139 first and second live births were analyzed. We found neonatal mortality rate of 32 per 1000 live births (95% CI: 29/1000-34/1000). Results from logistic regression model indicated increase in risk of neonatal mortality among neonates those born to young mothers aged 13–19 years compared with those whose mother‘s aged 20–34 years (aOR = 1.64, 95% CI = 1.34-2.02). We also found that neonates in second birth order were more likely to die than those in first birth order (aOR = 1.85:95%CI = 1.52-2.26). The risk of neonatal mortality among offspring of women who had a partner co-resident was 18% times lower as compared with offspring of mothers without a partner co-resident in the household (aOR = 0.82: 95%CI = 0.66-0.98). Short birth interval (<33 months) was associated with increased risk of neonatal mortality (aOR = 1.50, 95% CI =1.16-1.96) compared with long birth interval (> = 33 months). Male born neonates were found to have an increased risk (aOR = 1.34, 95% CI =1.13- 1.58) of neonatal mortality as compared to their female counterparts. Conclusions Delaying the age at first birth may be a valuable strategy to promote and improve neonatal he