The high viscosity of biodiesel fuel, caused by the presence of saturated fatty acid esters, limits its application, particularly at low temperatures. Supercritical fluid extraction (SFE) using carbon dioxide represents a promising method for selective fractionation, enabling the removal of high-viscosity saturated components and the enrichment of the fuel with less viscous unsaturated esters. However, the rational design of such processes requires a deep understanding of the interrelationship between flow hydrodynamics, thermodynamic conditions, and mass transfer in a supercritical medium. In this work, a comprehensive computational fluid dynamics (CFD) modeling study of the fractionation process was performed for a model ethyl oleate/ethyl palmitate mixture (25.28:74.72 wt.%) in supercritical CO2 at pressures of 11 and 14 MPa and a temperature of 40 °C. A three-dimensional model of a laboratory-scale extractor was developed using the ANSYS Fluent software environment. Since the target esters are absent from the standard material database, a custom property library and compiled User-Defined Function (UDF) routines were developed. These describe the temperature dependence of density, viscosity, heat capacity, and thermal conductivity for both the individual components and their mixture using established mixing rules. The calculations employed an Eulerian multiphase model, the realizable k–ε turbulence model, and species transport equations. The modeling revealed pronounced selectivity: under the chosen thermodynamic conditions, ethyl palmitate is extracted preferentially over ethyl oleate, with this difference becoming more pronounced as pressure increases. The developed and verified CFD model deepens the fundamental understanding of hydrodynamics and mass transfer during supercritical fractionation and serves as a basis for optimizing process parameters to produce biodiesel with reduced viscosity. The regime at P=14 MPa and t=40 °C provides the most favorable thermodynamic and hydrodynamic conditions for the selective removal of saturated esters.