Procalcitonin-guided antimicrobial decision-making has been shown to be safe in adult intensive care settings. Most antimicrobial exposure in neonatal units is in culture-negative conditions. We hypothesise that Procalcitonin aids antimicrobial stewardship efforts in suspected Late-Onset Neonatal Sepsis. Neonates were enrolled if they were aged over 72 h and were placed on antibiotics for a suspected infection. Procalcitonin levels were taken at set timepoints for the duration of antimicrobial exposure. Three subgroups were created: non-infectious episodes, blood culture-negative infectious episodes, and bloodstream infections. Eighty-five suspected infectious episodes were recruited across two tertiary neonatal and paediatric intensive care units. There was a significant difference between the median PCT in bloodstream infections (BSI) compared to non-infectious episodes (2.13 versus 0.26 µg/L, p < 0.001). A cut-off of 0.5 µg/L had sensitivity 92.9% and specificity 68% for bloodstream infections at 24 h. The difference between median PCT values at 24 h was significant (0.27 vs 7.08; p < 0.001) for feed intolerance vs. NEC Grade IIIa-IIIb subgroups. Procalcitonin levels taken 24 h following evaluation for late-onset neonatal infection are useful in out ruling BSI or severe Necrotising Enterocolitis. Up to 30% of antimicrobial exposure could be avoided with the use of Procalcitonin levels in low-risk neonates. This study demonstrates the utility of serial Procalcitonin measurements in antimicrobial stewardship efforts in the Neonatal Unit. Procalcitonin can be used to aid in antimicrobial decision making in suspected Late-Onset neonatal infection. Procalcitonin testing at twenty-four hours in episodes of Gastrointestinal deterioration can out rule Bells Grade III Necrotising Enterocolitis.