Pediocin, produced by certain lactic acid bacteria, has high antibacterial activity against Listeria monocytogenes and is therefore expected to be used as a peptide food preservative. In this study, a rapid and efficient method for recovering pediocin with antibacterial activity from a fusion protein with green fluorescent protein (GFP) produced by Escherichia coli was developed. After cell lysis, the concentrated fusion protein contained in the insoluble fraction was solubilized and desalted, and pediocin was cleaved from GFP by a protease factor Xa treatment. As pediocin exhibited strong adsorption to various membranes and a column matrix, and was presumed to adsorb to GFP, it was difficult to efficiently collect the pediocin with column purification and filtrations including ultrafiltration. Heating the mixture in boiling water was found to be an effective method to selectively remove GFP followed by centrifugation. Because pediocin is highly thermostable, soluble pediocin with high antilisterial activity was retained in the recovered supernatant. This study demonstrates that recombinant pediocin can be recovered rapidly and efficiently by the heat denaturation of cleaved fusion partner and centrifugation.