The Thompson Zoo is operated by the Thompson Zoological Society, a non-profit organization registered as a charitable organization. The society was set up with the purpose of operating and maintaining the Thompson Zoo.

While the City of Thompson has been the major source of funding, the Board of The Thompson Zoo is constantly faced with the challenge of finding other sources of funding for capital projects. To this end a Sponser An Animal program exists and other donations are gratefully accepted. All such funds are deposited into a trust fund created for that purpose. In addition, volunteers are always welcome.