Membrane active peptides (MAPs) have potential applications in drug delivery systems and as antimicrobials. We previously showed that a cationic comb-type copolymer, poly(allylamine)-graft-dextran (PAA-g-Dex), forms a soluble inter-polyelectrolyte complex with an anionic MAP, the E5 peptide, resulting in significant enhancement of the membrane disruption activity of E5. In this study, we designed a novel comb-type cationic copolymer composed of a PAA main chain and thermoresponsive poly( N-isopropylacrylamide) graft chains (PAA-g-PNIPAAm). We hypothesized that the thermoresponsive hydrophilic/hydrophobic transition of the grafted polymer would regulate the membrane disruption activity of E5 peptide. Both the binding affinity of the complex and the membrane disruption activity of E5/PAA-g-PNIPAAm were found to be enhanced above the phase transition temperature of the grafted chain. Our analysis suggests that the hydrophilic/hydrophobic environment around the cationic polymer chain plays important roles in the enhancement of the activity of the anionic peptide.