The study was aimed at screening, understanding, and optimizing product variability of dutasteride-loaded Eudragit E nanoparticles prepared by solvent displacement using Plackett-Burman screening and a central composite design. The independent process and formulation factors selected included: drug loading (%), solute concentration (mg/mL), Soluplus concentration (mg/mL), injection rate (mL/min), organic solvent type (methanol or ethanol), stirring rate (rpm), and organic-to-aqueous phase volume ratio. Among these factors, solute concentration was associated with increased particle size, broad particle size distribution, and enhanced entrapment efficiency. On the other hand, Soluplus concentration played a role in decreasing particle size, narrowing particle size distribution, and reducing entrapment efficiency. Other formulation and process factors did not have a significant impact on nanoparticle properties, assuming they were within the limits used in this study. The optimized formulation was achieved with 20 mg/mL solute and 3.22 mg/mL Soluplus, and the observed responses were very close to the values predicted using the response surface methodology. The results clearly showed that quality by design concept could be effectively applied to optimize dutasteride-loaded Eudragit E nanoparticles.