Objective:To evaluate the efficacy and risks of complications of pulse dosing of topical 5-fluorouracil (5-FU) in the treatment of corneal intraepithelial neoplasia (CIN), and conjunctival squamous cell carcinoma (SCC).Design:Prospective, noncomparative case series.Participants:Fifteen patients with histological evidence CIN or SCC of the conjunctiva and cornea were identified by tumor biopsy.Methods:All patients clinically evident of CIN, or SCC were evaluated, with maximum 30 months of follow-up were treated with pulsed dosing of 1% 5-FU. Treatment cycles were defined as four times per day for 4 days using the medication followed by 30 days without medication. The number of initial treatment was six cycles.Results:The mean age of the 15 patients was 50.8 years (range 25–78 years). Excision biopsy proved seven cases as CIN, and eight cases as locally invasive SCC. All patients remained disease free with a mean follow-up of 14.53 months (range 6–30 months). Additional chemotherapy was given after the initial treatment cycles, only for one case. 5-FU caused mild temporary local irritation, but no long-term intraocular or extra ocular complications.Conclusions:Adjuvant 1% topical 5-FU appears to be effective in the prevention of recurrence of conjunctival or corneal CIN and SCC after excision biopsy. Our results indicate that at least six cycles of topical 1% 5-FU is required to prevent local recurrence in the long term. It is well-tolerated and an effective method of treatment. No complications that would preclude use of our dose regimen were noted.