Background/Objectives: Mycophenolic acid (MPA) is used as part of first-line combination immunosuppressive therapy for renal transplant recipients. Personalized dosing approaches are needed to balance efficacy and minimize toxicity due to the pharmacokinetic variability of the drug. In this study, population pharmacokinetic (PopPK) modeling and machine learning (ML) techniques are coupled to provide valuable insights into optimizing MPA therapy. Methods: Using data from 76 renal transplant patients, two PopPK models were developed to describe and predict MPA levels for two different formulations (enteric-coated mycophenolate sodium and mycophenolate mofetil). Covariate effects on drug clearance were assessed, and Monte Carlo simulations were used to evaluate exposure under normal and reduced clearance conditions. ML techniques, including principal component analysis (PCA) and ensemble tree models (bagging and boosting), were applied to identify predictive factors and explore associations between MPA plasma/saliva concentrations and the examined covariates. Results: Total daily dose and post-transplant time (PTP) were identified as key covariates affecting clearance. PCA highlighted MPA dose as the primary determinant of plasma levels, with urea and PTP also playing significant roles. Boosted tree analysis confirmed these findings, demonstrating strong predictive accuracy (R² > 0.91). Incorporating saliva MPA levels improved predictive performance, suggesting that saliva may be a complementary monitoring tool, although plasma monitoring remained superior. Simulations allowed exploring potential dosing adjustments for patients with reduced clearance. Conclusions: This study demonstrates the potential of integrating machine learning with population pharmacokinetic modeling to improve the understanding of MPA variability and support individualized dosing strategies in renal transplant recipients. The developed PopPK/ML models provide a methodological foundation for future research toward more personalized immunosuppressive therapy.