The vasodilator effect of the semi-essential amino acid, L-arginine (LA) is crucial in the clinical management of angina pain and erectile dysfunction. Moreover, the limited bioavailability and the drug’s polar nature navigate the development of new formulation strategies for effective transdermal delivery, especially for the penile route. Thus, herein, we prepared the L-arginine–phosphatidylcholine (LA–PC) complex by solvent evaporation technique and converted it into a thermoresponsive gel (LA–PC gel). The optimized complex was selected for the preparation of gel using poloxamer 407, lactic acid, and purified water. Simultaneously we prepared the LA thermoresponsive gel (LA gel). The gels were characterized for their appearance, particle size, pH, osmolality, spreadability, SEM, FTIR, viscosity, TEM, viscoelastic properties, and skin permeability using the Strat-M® membrane at low pH for effective and safe penile and vaginal delivery. We observed that the LA–PC gel showed the smallest droplet size (<100 nm), a zeta potential of −59 mV indicates its stability with good viscoelastic behavior. The in vitro skin permeation reveals that; at 15 min, the permeation of LA for LA–PC gel, was 33.20% with a flux of 2.19 mg/cm2/min, and in the case of LA gel, the permeation of LA was only 18% at 45 minutes with a flux of 1.02 mg/cm2/min. The in vitro cytocompatibility was conducted using an L-929 cell line, and we found that both gels were nontoxic up to 100 µg/mL concentration. In summary, LA–PC gel could have a significant impact on the quick and sustained release, compared to LA gel.