This study aims to produce electrospun cellulose acetate (CA) membrane as the alternative supporting medium for a separation of crude polysaccharides by electrophoresis and a screening of their antibacterial activity. Among the tested conditions of fabrication, electrospun CA membrane at 57% porosity showed the best separation of each polysaccharide from the standard mixture and the crude extract of Aloe vera via electrophoresis. As compared with the commercial CA membrane, the produced electrospun CA membrane demonstrated more separated spots of polysaccharides. The antibacterial activity of the electrophoretic polysaccharide was also determined against Escherichia coli and Staphylococcus aureus as the inhibition zone after the bacterial culture agar was overlaid on the membrane and incubated for 24 h. The results of this study suggested the potential application of electrospun CA membrane combining with electrophoresis as a simple method for separating crude polysaccharides and screening for their antibacterial activity.