The National Fish Hatchery System was established by the U.S. Congress in 1871 through the creation of a U.S. Commissioner for Fish and Fisheries. The System is now administered by the U.S. Fish and Wildlife Service, an agency within the United States Department of the Interior.

The original purpose of the sytem was to provide domestic food fish to replace declining native fish populations. The role of the System has changed greatly over the past 30 years. Major responsibilities now include helping to recover species listed under the Endangered Species Act, restoring native aquatic populations, mitigating for fisheries lost as a result of federal water projects, and providing fish to benefit Indian Tribes and national wildlife refuges. The System is currently comprised of 70 National Fish Hatcheries, 9 Fish Health Centers, and 7 Fish Technology Centers.

Also see the List of National Fish Hatcheries in the United States.