The City of Sioux Falls owns the infrastructure, land, and all assets associated with the Zoo and Museum and maintains the grounds.

The Zoological Society of Sioux Falls, a non-profit, operates the facility, manages the animal collection, and maintains the grounds within the exhibit.

The Zoological Society of Sioux Falls was established in 1957, and helped develop the Great Plains Zoo, which opened its doors to the public on June 30, 1963.

[10][11] In 2020, Elizabeth A Whealy was removed from her position due to reported working conditions, a bullying management style, and continual turnover under her direction.

'Whealy's departure comes weeks after city officials and the zoological society's board received an anonymous letter alleging Whealy had created a hostile work environment for zoo staff and used a "bullying management style.'"

[21] In 2019, the zoo renovated several yards on its eastern and southeastern perimeter into an Australian-themed exhibit, providing renovated homes to Red and Eastern Grey Kangaroos, Bennett's Wallabies, and emus, and brings New Guinea singing dogs, Bactrian Camels, sheep in a station-themed petting enclosure, and several species of Australian birds.

[22] As part of the zoo's current master plan, new lion, meerkat, and leopard exhibits are slated to open in the African Savannah area.

The project will also include renovations to the Roar Café, the Great Plains Zoo's restaurant, providing expanded seating capacity for guests and climate-controlled views into animal exhibits.