Cutaneous leishmaniasis is caused by different species of Leishmania parasites and its available treatments have not yet provided a strong consistent result. The weak response of current chemotherapeutics is due to their deficient effects on stealth parasites inside macrophages, rapid clearance from the site of action and systemic side effects in high doses. Liposomal formulation of anti-leishmanial drugs could overcome these problems. In this study, different liposomal formulations of three famous anti-leishmanial drugs: Glucantime®, miltefosine and paromomycin were prepared by a modified freeze-drying double emulsion method. Liposome size, zeta potential and encapsulation efficiency were evaluated, and their imaging was carried out by means of atomic force microscopy. Three formulations were evaluated in vivo by subcutaneous injection into skin lesions caused by Leishmania major in BALB/c mice. Encapsulation efficiency of prepared liposomes was up to 90%; however, they inherited a bimodal size distribution that caused their encapsulation efficiency to decrease to 50% during filtering sterilization. Besides, the effect of surface charge was significant on preparation procedure, size and encapsulation efficiency. All three formulations reduced amastigote counts and lesion size but only miltefosine-loaded formulations had significant therapeutic effects compared with control group (p < 0.05).