Background and Objective: With improved survival in neonates with meconium aspiration syndrome (MAS), the focus is currently on mitigating the morbidities. The objective of this study was to predict factors determining prolonged hospital stay in neonates with MAS. Materials and methods: It was a retrospective cohort from five centres of south India between 2018 and 2020. Neonates ≥35 weeks of gestation admitted to NICU with the diagnosis of MAS and requiring oxygen beyond 24 hours of life were included in the study. The morbidities in the neonates with stay ≤7 days (short stay) were compared with >7 days (prolonged stay). Logistic regression by the backward stepwise method was used for predictive score creation. Results: Out of 347 neonates with MAS discharged home, 103 (29%) had a short stay and 244 (71%) had prolonged stay. The primary support beyond O2 (CPAP/MV) (42% vs 83%, p<0.001), FiO2 at 1hr>30% (45% vs 87%, p<0.001), HIE stage 2 or 3 (2% vs 27%, p<0.001), moderate-severe PPHN (3% vs 31%, p<0.001) were independent factors associated with prolonged stay on logistic regression. A prediction model was devised using weighted scores of these four associated morbidities. The clinical score thus developed had 83% sensitivity, 68% specificity for the prediction of prolonged stay [AUC- 82, 95% CI (78-87), p<0.001]. Conclusion: More than two-thirds of neonates with MAS had prolonged stay. The primary support beyond oxygen, Fio2 requirement >30%, Moderate to severe PPHN, HIE stage 2 or 3 were predictive of prolonged stay in neonates with MAS.