Biodegradable poly[(glycine ethyl ester)-(phenylalanine ethyl ester) phosphazene](PGPP) microparticles were fabricated by electrohydrodynamic atomization to apply drug release test. Atomization parameters such as applied voltage, polymer concentration, and molecular weight were investigated to inspect their effects on the size and morphology of microparticles. The average diameter of PGPP microparticles decreased as increasing applied voltage and solution flow rate. Dichloromethane/dioxane mixture shows better results for the preparation of microparticles than single solvent owing to the different PGPP solubility in solvent. Blending PGPP polymers with proper molecular weights not only favored the production of spherical PGPP microparticles via electrohydrodynamic atomization, but also provided a way to adjust drug (rifampicin) release behavior. Drug-loaded biodegradable polyphosphazene microspheres can be fabricated via electrohydrodynamic atomization, which has potential use in biomedical applications.