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Topical 5-fluorouracil (5-FU) is used for the treatment of actinic keratosis and nonmelanoma skin cancer. Unfortunately, 5-FU per se shows a poor percutaneous permeation, thus reducing its anticancer effectiveness after topical administration. Therefore, we have constructed transfersomes, liposomes, and niosomes of 5-FU for topical applications in this investigation. Transfersomes were prepared by the solvent evaporation method, whereas liposomes and niosomes were constructed by reverse-phase evaporation method. The nanovesicles were characterized for particle size, shape, zeta potential, viscosity, entrapment efficiency, deformability, in-vitro permeation release, and kinetics and retention. Cytotoxicity study was carried out on HaCaT cells. Transfersomes (153.2 ± 10.3 nm), liposomes (120.3 ± 9.8 nm), and niosomes (250.4 ± 8.6 nm) were produced with a maximum entrapment efficiency of 82.4 ± 4.8, 45.4 ± 3.3, and 43.4 ± 3.2%, respectively. Moreover, transmission electron microscopy and atomic force microscopy assure the smooth and spherical shape of nanovesicles. Skin permeation and retention showed better permeability and retention than the nonvesiculized dosage form. The IC50 value of transfersomes (1.02 μmol/l), liposomes (6.83 μmol/l), and niosomes (9.91 μmol/l) was found to be far less than 5-FU (15.89 μmol/l) at 72 h. 5-FU-loaded transfersomes were found to be most cytotoxic on the HaCaT cell line in comparison with liposomes and niosomes. We concluded that vesiculization of 5-FU not only improves the topical delivery, but also enhances the cytotoxic effect of 5-FU. We have presented here a viable formulation of 5-FU for the management of actinic keratosis and nonmelanoma skin carcinoma.