More than 1,200 visitors per year visit the refuge. The facility is unstaffed, but is administered by the Wheeler National Wildlife Refuge in Decatur, Alabama. The cave itself is closed to the public.
Fern Cave NWR is named after the profusion of ferns the original explorers found in the Surprise Pit sinkhole. Another entrance features the federally endangered American Hart's-tongue fern (Phyllitis scolopendrium). The fern population has declined since 1985 from a high of twenty to only two plants due to the actions of illegal plant collectors.
Fern Cave itself is described as a "vertical and horizontal maze". There are 12 different levels connected by canyons and pits. The cave is approximately long and contains vertical drops of up to . The cave remains very inaccessible. At least one experienced spelunker has died in the cave.
There are five entrances to the cave although only four of them are within the Fern Cave NWR. The fifth entrance is on private land.
Approximately 200 species of animals use the refuge. Other than the endangered bats, the cave contains cave fish (Typhlichthys subterraneus), cave crayfish, banded sculpins (Cottus carolinae), bluegill (Lepomis macrochirus), yellow bullhead catfish (Ictalurus natalis), cave salamanders (Eurycea lucifuga), and northern slimy salamanders (Plethodon glutinosus). Outside of the cave, white-tailed deer, turkeys, squirrels, opossums, raccoons, and rabbits have been seen.
Fern Cave is not open to the public in order to protect the endangered bats which reside within. The remaining portion of the Refuge is open to the public, although its use is limited due to the rugged topography.
Even through the bats leave the cave nightly for food, the refuge recommends against viewing the emergence. The area around the cave entrances is steep and potential dangerous in the dark. Thus, the park closes around dusk.
Otherwise, there are opportunities for hiking, photography, and wildlife observation at the refuge.