A clinical methylcellulose sampling strip is one of the popular means for collecting gingival crevicular fluid (GCF) from dental patients for dental disease diagnosis. In this research, a microfluidic device for protein elution from a sampling strip was fabricated with poly (dimethylsiloxane) (PDMS) polymer. Electoelution experiments were performed with fluorescein isothiocyanate (FITC) dye labeled bovine serum albumin (BSA) and ovalbumin (OVA). The total amount of eluted protein is measured by quantitative fluorescence imaging. About 50% of the initial concentration of BSA and OVA was eluted by the ~20 V/cm electric field. Electroelution is an appealing method for protein elution; however, the thickness of the wet strip (~400 μm) introduces interesting practical difficulties. During the electroelution process, unsteady electrokinetic phenomena by the pressure driven flow and the pH change of the reservoirs were observed. Several possible solutions to these problems are still under investigation including modifying reservoirs and thin polymer film coating of PDMS channel surfaces. This electroelution device would be a useful component of a fully integrated micro total analysis system for oral fluid samples.