This study was aimed at assessing the potential use of emulsion electrospinning to prepare core-shell structured ultrafine fibers as carriers for therapeutic proteins. It focused on the effect of fiber structure on the release profiles and structural stability of encapsulated proteins. In the case of bovine serum albumin (BSA) which was selected as a model protein, poly-DL-lactide ultrafine fibers prepared by emulsion electrospinning using a lower volume ratio of aqueous to organic phase, showed higher structural integrity of core-shell fiber as assessed by laser confocal scanning microscope (LCSM). This structural property can reduce the initial drug burst and improved the ability of the device to provide sustained therapeutic action. Fickian release was observed for the initial 60% of protein release. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and size exclusion chromatography (SEC) were used to assess the primary structure of BSA. These studies indicated that ultra-sonication caused denaturation of protein molecules, while the core-shell structured electrospun fibers protected the structural integrity of encapsulated protein during incubation in the medium. Fourier transform infrared (FTIR) analyses showed that the electrospinning process had much less effect on the secondary structure of protein than ultra-sonication. In vitro degradation study showed that the protein release from fibers led to more significant mass loss, higher molecular weight reduction and larger molecular weight distribution of the matrix residues, compared with fibers without protein inoculation. These data suggest that emulsion electrospinning can provide a useful core-sheath structure, which may serve as a promising scaffold for sustainable, controllable, and effective release of bioactive proteins in tissue engineering and other applications.