Dose personalization improves patient outcomes for many drugs with a narrow therapeutic index and high inter-individuality variability, including busulfan. Non-compartmental analysis (NCA) and model-based methods like maximum a posteriori Bayesian (MAP) approaches are two methods routinely used for dose optimization. These approaches vary in how they estimate patient-specific pharmacokinetic parameters to inform a dose and the impact of these differences is not well-understood. Using busulfan as an example application and area under the concentration–time curve (AUC) as a target exposure metric, these estimation methods were compared using retrospective patient data (N = 246) and simulated precision dosing treatment courses. NCA was performed with or without peak extension, and MAP Bayesian estimation was performed using either the one-compartment Shukla model or the two-compartment McCune model. All methods showed good agreement on real-world data (correlation coefficients of 0.945–0.998) as assessed by Bland–Altman plots, although agreement between NCA and MAP methods was higher during the first dosing interval (0.982–0.994) compared to subsequent dosing intervals (0.918–0.938). In dose adjustment simulations, both NCA and MAP estimated high target attainment (> 98%) although true simulated target attainment was lower for NCA (63–66%) versus MAP (91–93%). The largest differences in AUC estimation were due to different assumptions for the shape of the concentration curve during the infusion phase, followed by how the methods considered time-dependent clearance and concentration–time points collected in earlier intervals. In conclusion, although AUC estimates between the two methods showed good correlation, in a simulated study, MAP lead to higher target attainment. When changing from one method to another, or changing infusion duration and other factors, optimum estimated exposure targets may require adjusting to maintain a consistent exposure.