Acyclovir (ACR) is considered the gold standard drug for the treatment of skin viral infections caused by the herpes simplex or varicella-zoster virus. However, topical therapy with ACR is hindered by its poor skin penetrability, thus necessitating high doses and frequent administrations. This study was proposed to formulate a modified lipid-coated chitosan nanocomplexes (LCNCs) of acyclovir (ACR), containing span 80 and TPGS, to boost the dermal delivery of ACR and improve the therapeutic outcomes. LCNCs were formulated through a self-assembly method, and the statistical analysis and the optimization were performed via a general 23 factorial design. Three formulation variables were selected; namely, the amount of chitosan (A), the amount of glyceryl monooleate (GMO) (B), and span 80: D-α-tocopheryl polyethylene glycol succinate (Vitamin ETPGSorTPGS) ratio (C). Four measured attributes were determined; viz., the particle size (PS) in nm, the polydispersity index (PDI), the zeta potential (ZP) in mV, and the entrapment efficiency percentages (EE%). The optimal formulation (LCNCs 8), formulated with 600 mg chitosan, 120 mg GMO, and 3:1 span 80: TPGS ratio, possessed PS of 177.50 ± 1.41 nm, PDI value of 0.28 ± 0.02, ZP of −10.70 ± 0.85 mV, and EE% of 77.20 ± 2.40 %, and was able to sustain ACR release over 24 h. Transmission electron microscopy displayed LCNCs architecture as a polymeric core of chitosan with a lipid coat of GMO, and the solid-state characterization results confirmed the dispersion of ACR in LCNCs. The ex vivo permeation study and the in vivo dermatokinetics profile verified the boosted accumulation of ACR in the skin via LCNCs, while the confocal laser scanning microscopy revealed the heightened penetrability of LCNCs. The topical application of LCNCs demonstrated a safe profile via the modified Draize test and histopathological examinations. Inclusively, ACR-loaded LCNCs could be a promising topical formulation with an advanced dermal delivery status for the treatment of skin viral infections.