Cystinosis is an orphan disease caused by a genetic mutation that leads to deposition of cystine crystals in many organs including cornea. Ophthalmic manifestation of the disease can be treated with hourly instillation of cysteamine eye drops. The hourly eye drop instillation is tedious to the patients leading to poor compliance and additionally, significant degradation of the drug occurs within one week of opening the bottle, which further complicates this delivery approach. This paper focuses on designing a contact lens to treat the disease with improved efficacy compared to eye drops, and also exploring safety of the drug eluding contact lens in an animal model. Our goal is to design a lens that is safe and that can deliver a daily therapeutic dose of cysteamine to the cornea while retaining drug stability. We show that cysteamine diffuses out rapidly from all lenses due to its small size. Vitamin E incorporation increases the release duration of both ACUVUE®OASYS® and ACUVUE® TruEyeTM but the effect is more pronounced in TruEyeTM likely due to the low solubility of vitamin E in the lens matrix and higher aspect ratio of the barriers. The barriers are not effective in hydrogel lenses, which along with the high aspect ratio in silicone hydrogels suggests that barriers could be forming at the interface of the silicone and hydrogel phases. The presence of vitamin E has an additional beneficial effect of reduction in the oxidation rates, likely due to a transport barrier between the oxygen diffusing through the silicone channels and drug located in the hydrogel phase. Based on this study, both Acuvue®OASYS® and ACUVUE® TruEyeTM can be loaded with vitamin E to design a cysteamine eluting contact lenses for effective therapy of cystinosis. The lenses must be worn for about 4–5 hr. each day, which is less than the typical duration of daily-wear. The vitamin E and cysteamine loaded lenses did not exhibit any toxicity in a rabbit model over a period of 7-days.