Purpose: Vision-threatening ocular inflammation can be a devastating complication of granulomatosis with polyangiitis (GPA). Here we performed a retrospective observational study to describe the safety and efficacy of treating scleritis and uveitis with either cyclophosphamide or rituximab in GPA. Methods: A chart review of patients diagnosed with GPA-associated scleritis or uveitis, treated with either cyclophosphamide or rituximab as the final therapy at our clinic, was conducted. A total of 1 year of follow-up visits was required for inclusion in the study. Results: Thirteen patients (19 eyes) suffering from GPA-associated scleritis and/or uveitis were identified. As the final therapy, rituximab was administered to 9 patients and cyclophosphamide to 4. Mean duration of follow-up was 55 months (range 16–23 months). Remission was observed in all patients. Three patients had a flare of scleritis after the completion of therapy, and they were restarted on their respective agents. One patient had a flare of retinal vasculitis during rituximab therapy. One patient on cyclophosphamide experienced transient leukopenia. No adverse side effects of rituximab were noted throughout the course of treatment. Conclusions: Cyclophosphamide and rituximab are safe and effective agents for controlling scleritis and uveitis associated with GPA, with eventual progression towards steroid-sparing remission.