In the plasma membranes of eukaryotic cells, relatively ordered lipid–protein domains can be formed. The characteristics of the interaction of domains can have a significant effect on the processes that require the co-localization of several membrane proteins. The ordered lipid bilayer is thicker than the surrounding disordered membrane. Therefore, it is expected that elastic deformations arise at the boundary of ordered domains, aiming at smoothing the jump in bilayer thickness. The typical length of the deformations equals several nanometers, and, as two domains approach each other, the deformations induced by their boundaries begin to overlap, thereby leading to the effective lateral interaction. In this work, we theoretically considered the influence of amphipathic peptides, adsorbed on the membrane, on the interaction energy of ordered domains. Amphipathic peptides can partially incorporate into the membrane, inducing elastic deformations therein. We used the theory of lipid membrane elasticity to analyze the deformation energy of various configurations of ordered domains and amphipathic peptides. In a membrane without peptides, it is necessary to overcome some energy barrier to bring two parallel boundaries of ordered domains into contact with each other. According to the results of our calculations, the presence of amphipathic peptides in a membrane leads to a severalfold increase in the height of this energy barrier. Thus, amphipathic peptides should significantly hinder the fusion of ordered domains and thereby contribute to the stabilization of the ensemble of nano-domains.