Imiquimod has been demonstrated to be rather effective in patients with anal as well as perianal high-grade squamous intraepithelial lesions (HSILs). Nevertheless, until now the intra-anal use of imiquimod has been considered off-label. The aim of this study is to review the clinical evidence related to the intra-anal use of imiquimod in the treatment of human papillomavirus-related anal lesions. A systematic search in PubMed and Scopus was performed. In total, 422 patients were included. The most common referred comorbidity was HIV infection (281 patients, 66.6%). The principal clinical entities, which were treated with intra-anal imiquimod, were HSILs. The most frequent formulation was self-applied imiquimod cream. In the HSIL group, there was complete healing in 74 patients (35%) and partial in 44 patients (20.9%), while in the wart group, there was complete healing in 128 patients (67%). Recurrence of HSIL was present in 19 patients (15%), while in cases with warts recurrence was present in 38 patients (19.8%). The most common adverse events were pain, itching, and burning sensation. In conclusion, the adverse effects associated with the intra-anal use of imiquimod seem to be minor. The present clinical evidence suggests that imiquimod may be proposed as effective, safe, and relatively well tolerated treatment.