Budesonide (BUD) loaded ethylcellulose (EC)-core/Eudragit S100-shell nanofibers (BUD-core/shell-NFs) have been successfully prepared using a coaxial electrospinning technique. The drug encapsulation efficiency was 90.48%. SEM and TEM analysis showed that fine core shell structured nanofibers with an average diameter 190 nm and uniform core diameters 74 nm were prepared. The BUD-loaded Eudragit S100/EC composite nanofibers (BUD-NFs) were prepared using a blend electrospinning method and used as a control. In vitro release tests in HCl 0.1 N, phosphate buffer solutions pH 6.8 and 7.4 were studied. Moreover, the colon-specific characteristics were directly proven in vivo by the content of BUD in different segments of the gastrointestinal (GI) tract in rats after oral administration. Taken together, the results confirmed that BUD-core/shell-NFs had desired pH-dependent drug release profile, displayed a sustained and complete drug release in the colon, as well as protected BUD from being released completely in the upper portion of the GI tract. Compared with BUD-NFs, the BUD-core/shell-NFs have much better potential to be developed as oral colon-specific drug delivery system (OCDDS) to overcome the disadvantages of current oral formulations of BUD.