The delivery of drugs to specific target tissues and cells in the brain poses a significant challenge in brain therapeutics, primarily due to a limited understanding of how nanoparticle properties influence drug biodistribution and off-target organ accumulation. This study addresses the limitations of previous research by presenting a novel and innovative approach that utilizes a large dataset incorporating both numerical and categorical features. Unlike previous studies, which often suffer from inadequate data and accuracy, our focus is specifically on brain delivery in vivo testing. Through a systematic analysis of 403 data points, including measurements of brain and plasma area under the curve (AUC) following nanoparticle (NP) administration, we extensively characterized the chemical and physical properties of loaded drugs and NPs as carriers. Utilizing machine learning techniques and comprehensive literature data analysis, we developed accurate models for predicting NP delivery to the brain. Our analysis employed various linear models, with a particular emphasis on the superior performance of linear mixed-effects models. These models demonstrated exceptional accuracy, as indicated by high R2 and adjusted R2 scores, in predicting the delivery of NPs to the brain. This breakthrough provides a valuable tool for guiding the design of nanocarriers in clinical applications, resulting in reduced experimental costs and the mitigation of unintended biological outcomes. To validate our models, we synthesised and administered two distinct NP formulations via intranasal (IN) and intravenous (IV) routes, further substantiating the efficacy of our proposed models. Among the various modeling approaches, linear mixed-effects models exhibited superior performance in capturing underlying patterns.