There are many band-operated schools in Manitoba. These are schools funded at the federal level by the Government of Canada but managed by one or more of the First Nations band governments. In accordance with the treaty arrangements between the federal government and most individual First Nations, band-operated schools must be administered by locally elected School boards, and operate outside the direct control of the local chief and band council.

While there is no legislative requirement that band-operated schools follow provincial curricula, or adhere to the Manitoba Public Schools Act or the Manitoba Education Administration Act, most of them do operate very similarly to provincial schools. The more closely a federal school follows provincial curricula, the more readily its students can transfer into the provincial system. Graduation from First Nation high schools that retain accreditation is recognized by post-secondary institutions.

In First Nation schools, provincial professional organizations such as the Manitoba Teachers' Society (MTS) are noticeably absent. Of the fifty-one First Nations communities that operate federal schools, only two have teachers who are members of the provincial union, while all other public school teachers are automatically members under the Public Schools Act and Education Administration Act. The exceptions are members of the Nelson House Teachers' Association in Nisichawayasihk Cree Nation and the Sandy Bay Teachers' Association in Sandy Bay Ojibwa First Nation. The members of these two bargaining units are not entitled to the MTS pension and disability benefits plans, as no legislation exists that would allow them to participate.

List Birdtail Sioux Nursery School - Birdtail Sioux First Nation, Manitoba Sargeant Tommy Prince School - Brokenhead Ojibway Nation, Manitoba Wambdi Iyotake School - Canupawakpa Dakota Nation, Oak Lake, Manitoba Chemawawin School - Chemawawin Cree Nation, Manitoba Mahpiya Hdega School - Dakota Plains First Nation, Manitoba Dakota Tipi School - Dakota Tipi First Nation, Manitoba Dauphin River School - Dauphin River First Nation, Manitoba Ebb & Flow School - Ebb & Flow First Nation, Manitoba Pinaymootang School - Pinaymootang First Nation, Manitoba Charles Sinclair School - Fisher River Cree Nation, Manitoba Fox Lake School - Fox Lake Cree Nation, Manitoba Kistigan Wacheeng - Garden Hill First Nation, Manitoba Garden Hill First Nation High School - Garden Hill First Nation God's Lake Narrows First Nation School - God's Lake First Nation, Manitoba Keeseekoowenin School - Keeseekoowenin Ojibway Nation, Manitoba Lawrence Sinclair Memorial School - Kinonjeoshtegon First Nation, Manitoba Lake Manitoba School - Lake Manitoba First Nation, Manitoba Lake St. Martin School - Lake St. Martin First Nation, Manitoba Little Black River School - Little Black River First Nation, Manitoba Little Grand Rapids School - Little Grand Rapids First Nation, Manitoba Little Saskatchewan H.A.G.M.E. School - Little Saskatchewan First Nation, Manitoba Long Plain School - Long Plain First Nation, Manitoba Amos Okemow Memorial School - Manto Sipi First Nation, Gods River, Manitoba Sakastew School - Mathias Colomb First Nation, Pukatawagan, Manitoba Miskooseepi School - Bloodvein First Nation, Bloodvein, Manitoba Nisichawayasihk Neyo Ohtinwak Collegiate - Nisichawayasihk Cree Nation, Nelson House, Manitoba Otetiskiwin Kiskinwamahtowekamik - Nisichawayasihk Cree Nation, Nelson House, Manitoba Petit Casimir Memorial School - Northlands First Nation, Manitoba Donald Ahmo School - O-Chi-Chak-Ko-Sipi First Nation, Manitoba Joe A. Ross School - Opaskwayak Cree Nation, Manitoba Oxford House Elementary School - Oxford House First Nation, Manitoba 1972 Memorial High School - Oxford House First Nation, Manitoba Pauingassi School - Pauingassi First Nation, Manitoba Peguis Central School - Peguis First Nation, Manitoba Mikisew Middle School - Pimicikamak Cree Nation, Manitoba Otter Nelson River School - Pimicikamak Cree Nation, Manitoba Pine Creek School - Pine Creek First Nation, Manitoba Poplar River School - Poplar River First Nation, Manitoba Red Sucker Lake First Nation School - Red Sucker Lake First Nation, Manitoba Wapi-Penace School - Rolling River First Nation, Manitoba Ginew School - Roseau River Anishnaabe First Nation, Roseau River (Manitoba–Minnesota) St. Theresa Point Elementary School - St. Theresa Point First Nation, Manitoba St. Theresa Point High School - St. Theresa Point First Nation, Manitoba St. Theresa Point Middle School - St. Theresa Point First Nation, Manitoba Sagkeeng Anicinabe Community School - Sagkeeng First Nation, Manitoba Sagkeeng Anicinabe High School - Sagkeeng First Nation, Manitoba Sagkeeng Consolidated School - Sagkeeng First Nation, Manitoba Isaac Beaulieu Memorial School - Sandy Bay Ojibway First Nation, Manitoba Neil Dennis Kematch Memorial School - Sapotaweyak First Nation, Manitoba Peter Yassie Memorial School - Sayisi Dene Nation, Manitoba Abraham Beardy School - Shamattawa First Nation, Manitoba Sioux Valley School - Sioux Valley Dakota Nation, Manitoba Indian Springs School (Manitoba) - Swan Lake First Nation, Manitoba Chief Sam Cook Mahmuwee Education Centre - Tataskweyak Cree Nation, Manitoba Chief Clifford Lynxleg Anishinabe School - Tootinawaziibeeng Treaty Reserve, Manitoba George Knott School - Wasagamack First Nation, Manitoba Waywayseecappo Community School - Waywayseecappo First Nation, Manitoba Wuskwi Sipihk School - Wuskwi Sipihk First Nation, Manitoba George Saunders Memorial School - York Factory First Nation, Manitoba

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