Objective The aim was to measure plasma l-carnitine concentration in healthy and septic neonates, and the relation between l-carnitine concentration and gestational age, birth weight, and presence of neonatal sepsis. Background Neonatal sepsis and endotoxemia result in impaired lipid metabolism and hepatic energy generation from fatty acid oxidation which could put those neonates at risk of l-carnitine deficiency. Materials and methods The study was carried out at the Menoufiya University Hospital over 1 year on 40 of healthy and septic neonates. All neonates were subjected to full history taking, clinical examination, and laboratory investigations included measurement of serum l-carnitine level, sepsis workup, and other laboratory investigations. Results Our study included 40 neonates, They were divided into four groups. Group 1: 10 healthy preterm neonates with a mean gestational age of between 33.50±1.18 weeks and mean birth weight of between 1.82±0.18 kg. Group 2: 10 healthy full-term neonates with a mean gestational age of between 38.80±1.03 weeks and mean birth weight of 2.98±0.23 kg. Group 3: 13 septic preterm neonates with a mean gestational age of between 33.46±1.13 weeks, and mean birth weight of 1.95±0.31 kg. Group 4: seven septic full-term neonates with a mean gestational age of between 38.57±1.27 weeks and mean birth weight of between 3.00±0.34 kg. Septic neonates groups (groups 3 and 4) have a low level of l-carnitine than healthy neonates groups (groups 1 2) and among septic groups the septic preterm neonates group (group 3) have a high level of l-carnitine than septic full-term neonates group (group 4). Also among healthy groups, the healthy preterm neonates group (group 1) have a high level of l-carnitine than healthy full-term neonates group (group 2). There was no correlation between l-carnitine and maternal age, gestational age, birth weight, and laboratory investigations in all groups. Conclusion There is a significant decrease of serum l-carnitine level in septic neonates, so they need assessment and supplementation. There is no correlation between serum level of l-carnitine and both gestational age and birth weight.