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A female in her early 20s with bilateral congenital aniridia-associated keratopathy (AAK) and progressive limbal stem cell deficiency (LSCD) presented with recurrent epithelial defects in the left eye for which she underwent cadaveric allogeneic simple limbal epithelial transplantation (allo-SLET) with lateral paramedian tarsorrhaphy. Postoperatively, topical and systemic immunosuppression with topical corticosteroids and oral cyclosporine was initiated. The ocular surface stabilised after surgery; however, an episode of epithelial rejection occurred at 4 months which resolved with intensified corticosteroid therapy and intravenous methylprednisolone. Subsequent cataract surgery was performed and the ocular surface remained stable. Best-corrected visual acuity improved from 20/600 to 20/160 and remained stable over a 2.5-year follow-up. This case highlights allo-SLET as an effective option for advanced bilateral AAK and the need for long term immunosuppression to prevent episodes of epithelial rejection and recurrence of LSCD.