Background. Lichen planopilaris is the leading cause of cicatricial alopecia, and its management is challenging for dermatologists. It is a cell‐mediated autoimmune disorder in which activated T‐lymphocytes attack hair follicles. Aim. To compare the efficacy and safety of methotrexate versus azathioprine, two medications that affect lymphocyte function, in treating LPP. Methods. 32 LPP patients were randomly assigned to receive either 15 mg/week methotrexate or 2 mg/kg azathioprine for six months. Treatment efficacy was evaluated using the Lichen Planopilaris Activity Index (LPPAI), trichoscopy, and photography after 2, 4, and 6 months of treatment. Results. Both methotrexate and azathioprine groups showed significant improvements in LPPAI (P < 0.001) and perifollicular scaling on trichoscopy (P < 0.01). However, the two groups had no significant difference during the study. The azathioprine group significantly improved perifollicular erythema on trichoscopy (P = 0.002), but this was not significantly different from the methotrexate group (P = 0.69). Photographic assessment showed that more than 75% of patients in both groups improved without significant differences between the two groups. Conclusion. Methotrexate and azathioprine are two antilymphocyte medications which are both equally effective and well‐tolerated for managing LPP. This trial is registered with IRCT20191006045005N2.