It was first built in 1938 and then rebuilt in 1957. As part of the Fish Hatchery Production Plan, a new hatchery was built on Division-owned property approximately one mile from the existing hatchery. Construction began in 2001 and was completed in May, 2002.

The hatchery produces rainbow and cutthroat trout and kokanee. These are stocked in central Utah waters, Strawberry Reservoir and Bear Lake. The hatchery previously had a capacity to produce 60,000 pounds of fish annually. With construction of the new hatchery, this capacity more than doubled. Over 700,000 Bonneville cutthroat trout (Bear Lake strain) eggs were moved to the new station after it was constructed. The majority of these were stocked in Strawberry Reservoir. Production in 2003 was 1,888,639 trout weighing 145,970 pounds. By 2012, 236,000 pounds of cold-water fish were being produced at Fountain Green Hatchery.

The Central Utah Project and other reclamation projects created many reservoirs in Utah. These flatwater areas provide for a variety of water-related recreation opportunities including fishing. Most reservoir fisheries are heavily used and not able to sustain themselves through natural recruitment, requiring management programs dependent on stocking hatchery-reared fish. Fish stocking demands in Utah for reclamation projects have been met in the past through both State and Federal hatcheries. CUPCA identifies funding for planning and implementing improvements to existing hatcheries and/or the development of new fish hatcheries to increase production of warm-water and cold-water fish for areas affected by the Colorado River Storage Project in Utah.