5-trans Fluprostenol is primarily used in medical and veterinary applications due to its prostaglandin analog properties. In human medicine, it is utilized in ophthalmology for the treatment of glaucoma and ocular hypertension, helping to reduce intraocular pressure by increasing the outflow of aqueous humor. This makes it a valuable therapeutic agent for preventing optic nerve damage and preserving vision in patients with these conditions.

In veterinary medicine, it is employed in reproductive management, particularly in livestock. It is used to induce luteolysis, synchronize estrus, and facilitate timed artificial insemination, improving breeding efficiency in cattle and other animals. Additionally, it aids in the treatment of certain reproductive disorders, enhancing fertility and herd management practices. Its role in both medical and veterinary fields underscores its importance as a versatile and effective prostaglandin analog.