Early prediction of neonates' survival and Length of Stay (LOS) in Neonatal Intensive Care Units (NICU) is effective in decision-making. We developed an intelligent system to predict neonatal survival and LOS using the "Case-Based Reasoning” (CBR) method. We developed a web-based CBR system based on K-Nearest Neighborhood (KNN) on 1682 neonates and 17 variables for mortality and 13 variables for LOS and evaluated the system with 336 retrospectively collected data. We implemented the system in a NICU to externally validate the system and evaluate the system prediction acceptability and usability. Our internal validation on the balanced case base showed high accuracy (97.02%), and F-score (0.984) for survival prediction. The root Mean Square Error (RMSE) for LOS was 4.78 days. External validation on the balanced case base indicated high accuracy (98.91%), and F-score (0.993) to predict survival. RMSE for LOS was 3.27 days. Usability evaluation showed that more than half of the issues identified were related to appearance and rated as a low priority to be fixed. Acceptability assessment showed a high acceptance and confidence in responses. The usability score (80.71) indicated high system usability for neonatologists. This system is available athttp://neonatalcdss.ir/. Positive results of our system in terms of performance, acceptability, and usability indicated this system can be used to improve neonatal care.