Microcapsules, containing the pharmaceutical substance shikonin, were prepared by the solvent evaporation method in order to enhance shikonin stability (reduce photo-oxidation, polymerization), decrease its hydrophobicity and control its release rate. The effect of various parameters, such as type of polymer, type and concentration of surfactant, solvent volume and mastic gum (Pistacia lentiscus resin) content/concentration as core additive, on the characteristics of the produced microcapsules and the release rate of shikonin, were experimentally investigated. Among the polymers tested for matrix, ethylcellulose (EC) of viscosity 10 cp was the most successful; EC 100 cp and mastic gum result in larger/compact particles with no pores and much slower release. Sodium dodecyl sulphate (SDS) results in microcapsules with desirable morphological and physicochemical characteristics, while polyethylene glycol (PEG) and polyvinyl alcohol (PVA) are not indicated as surfactants in shikonin microencapsulation. Decreasing the solvent volume (dichloromethane) results in increased mean particle size and, thus, in slower release rate of shikonin, while the incorporation of mastic gum in the capsule core results in better control of shikonin release. Finally, the combination of EC 10 cp as matrix, mastic gum as core additive, low dichloromethane (DCM) volume and low SDS concentration results in microcapsules with the best characteristics in terms of efficiency, loading, release and particle size distribution.