Introduction: Symptoms of sepsis are non-specific among neonates and diagnosis requires a high index of suspicion. The study sought to evaluate the utility of procalcitonin (PCT) versus C-reactive protein (CRP) in diagnosing early-onset neonatal sepsis. Methods: This was a cross-sectional study in which neonates admitted to the neonatal intensive care unit, with signs suggesting sepsis were categorized according to an adapted criteria from Tollner's sepsis score and case definition of bloodstream infection as: ''highly probable'', ''probable'' and ''less probable''. Laboratory investigations including blood culture, complete blood count, PCT and CRP levels were done before first antimicrobial drug administration. Results: A total of 62 neonates less than 12 hours postnatal age (0.16-9.82 hours) were recruited. Proportion of neonates with PCT>2 ng/mL was 91% (20/22) in the ''highly probable'' group compared to 31.6% (6/19) in the ''probable group'' (p<0.001). Neonates with CRP>5 mg/L was 54.4% (12/22) in the ''highly probable'' group compared to 26.3% (5/19) in the ''probable group'' (p = 0.07). The receiver operator characteristics for PCT and CRP were; sensitivity (87.5% vrs 50%), specificity (63.0% vrs 72.2%), positive predictive value (44.1% vrs 37.5%) and negative predictive value (93.8% vrs 81.3%), respectively. Conclusion: PCT was a better predictive marker for neonatal sepsis within the first 12 hours of life than CRP in this setting, however, its low specificity relative to CRP suggests that neonates without patent infection are more likely to be incorrectly diagnosed with sepsis using this test.