Skin and soft tissue infections following surgical procedures are usually caused by a broad range of bacteria and are the major cause of septic complications and hospital mortality. Treatment of such wounds is a challenge often resulting from the transition from acute to chronic inflammation due to persistence of pathogenic microflora in the wound tissue. The study was aimed to assess the wound-healing activity of the ointment composition based on the dispersion of fullerene C60 (AFD) in the in vivo model of skin wound, to estimate the effects of AFD on the expression of cytokines as markers of regenerative processes, to determine antibacterial activity of the developed cationic peptides. AFD was obtained by tangential ultrafiltration and used to make an ointment composition. The BALB/c mice were used to model the skin injury. The cationic peptides (CPs) were synthesized by the solid-phase method using the Fmoc technology. Antibacterial effects of CPs and AFD were estimated by colony counting. It was found that the AFD-based ointment exerted wound-healing and anti-inflammatory activity. The minimum bactericidal concentrations (MBC) of the CPs most active against the E. coli Dh5α strain, AB-1, AB-2, AB-3, and ST-10, were 1.15, 0.11, 0.74, and 0.74 mM, respectively, while MBC of ampicillin was 0.7 mM. We assume that constructing the hybrid compounds/fullerene C60 conjugates with active CPs will be a promising area of the development of drugs for treatment of wounds complicated by bacterial infection.