Objective This study aimed to compare the ventilator-free days (VFDs) at day 28 and the short-term outcomes in neonates with and without ventilator-associated pneumonia (VAP and non-VAP groups). Study design We performed a cohort study in a Thai neonatal intensive care unit between 2014 and 2020 to identify the VFDs in VAP and non-VAP neonates. Univariate and multivariate analyses were performed. Results The incidences of VAP rates were 5.76% (67/1,163 neonates) and 10.86 per 1,000 (92/8,469) ventilator days. The medians (interquartile ranges [IQRs]) of gestational age and birth weight in the VAP versus non-VAP groups were 31 (27-35) versus 34 (30-38) weeks, and 1,495 (813-2,593) versus 2,220 (1,405-2,940) g (p < 0.001, both), respectively. The medians (IQRs) of VFDs at 28 days in the VAP and non-VAP groups were 5 (0-16) and 24 (20-26) days (p < 0.001). From the univariate analysis, the lower VFDs, longer ventilator days, and higher rates of moderate-to-severe bronchopulmonary dysplasia (BPD), postnatal steroids for BPD, length of stay, and daily hospital cost in the VAP group were significantly higher than in the non-VAP group. From the multivariate analysis, the VAP group had significantly lower VFDs (regression coefficient = -10.99, standard error = 1.11, p < 0.001) and higher BPD (adjusted risk ratio = 18.70; 95% confidence interval = 9.17-39.5, p < 0.001) than the non-VAP group. Conclusion Neonatal VAP lead to lower VFDs and a higher frequency of BPD. A multimodal strategy with a VAP prevention bundle care should be used in indicated cases to reduce the occurrence of neonatal VAP.