A non-water-soluble natural antibacterial peptide, gramicidin A, has been successfully incorporated into polyelectrolyte assemblies to elaborate biocidal thin films. For this, we used a double strategy, the first step of which consists of complexing the peptide by a non-denaturing anionic amphiphilic polysaccharide, namely a hydrophobically modified carboxymethylpullulan. We demonstrate that the use of this amphiphilic anionic derivative allows to efficiently solubilize the peptide in aqueous solution, without denaturation. The amount of peptide solubilized by the amphiphilic polysaccharide was optimized by systematically varying the hydrophobicity and the molar mass of the CMP derivative. In a second step, the negatively charged complex was layer-by-layer assembled with cationic poly(L-lysine) to form biofunctionalized thin films. The amount of peptide incorporated in the multilayers was controlled by changing the number of deposited complex layers, and was quantified by UV spectroscopy. The antibacterial activity of the resulting biofunctionalized films was evidenced against a gram-positive bacterium, E. faecalis. We demonstrated that the biocidal activity resulted from a double mechanism: contact between bacteria and the film surface, and release of the peptide into the solution surrounding the film. We also showed that the peptide was not completely removed from the film after rinsing, which insured preservation of the biocidal activity of the film surface.