Background Neonatal sepsis remains one of the leading causes of morbidity and mortality in neonates, especially in developing countries. Objectives To determine the prevalence, common bacterial pathogens, and the antibiotic susceptibility pattern of neonatal sepsis at the Lagos University Teaching Hospital (LUTH), Lagos, Nigeria. Methods This was a cross-sectional study of neonates who presented at the facility with symptoms and signs of sepsis from January 2017 to October 2017. Demographic and clinical data were extracted using a structured questionnaire. Blood culture, urine and CSF were collected and cultured on blood and MacConkey agar. Bacterial isolates were identified using Microbact 24E system and biochemical tests. Antibacterial susceptibility testing was done using the modified Kirby–Bauer disc diffusion method. Results Two hundred and ninety neonates were recruited during the study period. Seventy-three (25.2%) neonates had culture-proven sepsis. One (0.3%) neonate had meningitis and no neonates (0%) had confirmed urinary tract infection. Of the 73 neonates with positive blood cultures, 56 (76.7%) had early-onset sepsis and 17 (23.3%) had late-onset sepsis. Gram-negative bacilli accounted for 60.3% of all isolates. Predominantly isolated pathogens were Staphylococcus aureus (20.5%), CoNS (19.2%) and Klebsiella pneumoniae (13.7%). The isolates were most susceptible to levofloxacin and amikacin. Conclusions Neonatal sepsis is still a huge burden in the newborn. S. aureus, CoNS and K. pneumoniae are the prevalent pathogens in the local facility, with good susceptibility to levofloxacin and amikacin. Maintaining regular antibiotic surveillance for appropriate empirical antibiotics is important as part of neonatal care.