Neonatal medical data holds critical information within the healthcare industry, and it is important to analyze this data effectively. Machine learning algorithms offer powerful tools for extracting meaningful insights from the medical data of neonates and improving treatment processes. Knowing the length of hospital stay in advance is very important for managing hospital resources, healthcare personnel, and costs. Thus, this study aims to estimate the length of stay for infants treated in the Neonatal Intensive Care Unit (NICU) using machine learning algorithms. Our study conducted a two-class prediction for long and short-term lengths of stay utilizing a unique dataset. Adopting a hybrid approach called Classifier Fusion-LoS, the study involved two stages. In the initial stage, various classifiers were employed including classical models such as Logistic Regression, ExtraTrees, Random Forest, KNN, Support Vector Classifier, as well as ensemble models like AdaBoost, GradientBoosting, XGBoost, and CatBoost. Random Forest yielded the highest validation accuracy at 0.94. In the subsequent stage, the Voting Classifier—an ensemble method—was applied, resulting in accuracy increasing to 0.96. Our method outperformed existing studies in terms of accuracy, including both neonatal-specific length of stay prediction studies and other general length of stay prediction research. While the length of stay estimation offers insights into the potential suitability of the incubators in the NICUs, which are not universally available in every city, for patient admission, it plays a pivotal role in delineating the treatment protocols of patients. Additionally, the research provides crucial information to the hospital management for planning such as beds, equipment, personnel, and costs.