Minoxidil is effective in the management of androgenic alopecia. However, a new drug delivery system is needed to maximize its efficacy and minimize side effects associated with its conventional formulation. Minoxidil was encapsulated into transferosomes and transethosomes and their particle size, polydispersity index, drug entrapment efficiency and in vitro drug release profiles were studied. Skin permeability and deposition were evaluated using rat abdominal skin. The particle size of the transethosomes (69.8 ± 1.4 to 167.4 ± 16.7 nm) was significantly smaller than that of the transferosomes (148.0 ± 0.3 to 364.2 ± 5.0 nm). Drug entrapment efficiency was significantly lower for the transethosomes (23.7 ± 3.2 to 47.2 ± 1.3%) compared to the transferosomes (77.0 ± 1.3 to 79.2 ± 0.1%). The drug release pattern was biphasic with a burst phase followed by a sustained release one. The transferosomes and transethosomes containing oleic acid had the best ability to sustain drug release. Transferosomes and transethosomes had respectively 2.84- and 3.36-fold enhancement in drug skin permeability compared with the drug hydroalcoholic solution. In addition, drug skin deposition was 28.5- and 18-fold higher in the stratum corneum and 3.6- and 6.5-fold higher in the epidermis/dermis for transferosomes and transethosomes, respectively compared with the drug hydroalcoholic solution. The transethosomes containing oleic acid had the highest permeability through the skin, highest deposition in deep skin layers and lowest deposition in stratum corneum. Transethosomes enhanced skin permeability and retention might improve minoxidil efficacy in the treatment of androgenic alopecia and reduce its side effects.