This study evaluates the efficacy of the spray-drying technique in the bioengineering of phenytoin (PHT) containing poly(ε-caprolactone) (PCL) microcarrier intended for brain delivery for long-term treatment of epilepsy. Through orthogonally designed experiments, the optimal formulation and process variables for the preparation of PCL-microcarriers containing PHT were obtained. The produced microcarriers were characterized by coulter counter, scanning electron, scanning transmission electron microscopies, differential scanning calorimetry, powder X-ray diffraction, and in vitro release. The results showed that the produced microcarriers have a spherical structure, uniform size distribution, and a particle mean diameter of about 4.0 μm, which is suitable for brain delivery. The PHT was loaded as dispersed microcrystals within the PCL-microcarriers. From this system, PHT was released slowly into a buffer solution for approximately 14 days without any burst effect. These data suggested that PHT containing spray-dried PCL-microcarrier may be a promising drug delivery system for local brain delivery and long-term treatment of pharmacoresistant epilepsy.