Basal cell carcinoma (BCC) is the most common malignant skin tumor. While slowly growing, it can cause major skin disfigurement. Therefore, novel cosmetically acceptable treatment options, other than surgery require investigation. The aim of the study was to evaluate efficacy and safety of intralesional methotrexate (MTX) as a convenient modality for BCC treatment clinically and pathologicaly. A total of 20 patients with BCC of any clinical variant underwent intralesional MTX injection at a maximum 1 mL of 25 mg/mL MTX per session. Histopathological assessments were performed before and 1 month after treatment. Forty percent of patients showed >50% clinical improvement after 1–4 sessions. Intralesional MTX is a suitable and safe treatment modality for BCC and may be used as an adjuvant to surgery.