Acne is the pilosebaceous units' disorder. The most important cause of acne is the colonization of bacteria in the follicles. Among antibiotics, doxycycline-hyclate kills a wide range of bacteria. To prevent oral administration's side effects, overcome the barriers of conventional topical treatment, and improve the therapeutic effectiveness, doxycycline-hyclate was loaded into four niosomal formulations with different percentages of constituents (span 60 and cholesterol) prepared by the thin-film hydration method. Then, one of the four formulations with the most appropriate particle size of 362.88 ± 13.05 nm to target the follicles, percentage of drug entrapment efficiency of 56.3 ± 2.1%, in vitro drug release of 54.93 ± 1.99% after 32 hours, and the lowest permeation of the drug through the Wistar rat skin, was selected. Then, its toxicity on human dermal fibroblasts (HDF) by MTT method after 72 hours, its antibacterial activity against the main acne-causing bacteria via antibiogram test, and its effect on Wistar rat skin drug deposition were measured. Improved cell viability, increased antibacterial activity, and an approximately three-fold increase in drug deposition were the optimal niosomal formulation features relative to the free drug. Overall, this study demonstrated the ability of nano-niosomes containing doxycycline-hyclate to treat skin acne.