It's the first tripartite agreement with Ontario, and is based on similar agreements that have worked well in other provinces.
The memorandum of understanding is with the Nishnawbe Aski Nation, an organization that represents 49 First Nations communities across northern Ontario, many of them isolated and struggling with poverty and addiction.
The memo commits governments and First Nations to improving education so that it is on par with the rest of the province.
First Nations teachers, support staff and parents will have more input in curriculum and a larger presence in schools.
And signatories also commit to improving student safety and helping children who are living away from home while they go to school.
Many First Nations children drop out of school or run into difficulties when they need to move hundreds of kilometres away from their reserves in order to pursue their education.
Aboriginal Affairs Minister Bernard Valcourt, Ontario Education Minister Liz Sandals and Assembly of First Nations National Chief Shawn Atleo travelled to the Mattagami First Nation, south of Timmins, Ont., to meet area chiefs and sign the agreement.
"By working collaboratively we will be better able to prepare our students with the self-confidence and educational opportunities they need to reach their educational goals and achieve their full potential," said Grand Chief Harvey Yesno.
The federal government's education agenda has not been universally well received.
Widespread protest has greeted the Conservative plan for legislation next year that would give First Nations more control over education through school-board type arrangements.
The protesters say the government is being too prescriptive and heavy-handed, while ignoring the need for funding they say is necessary to set First Nations schools on a equal footing with provincial schools.
On Tuesday, a spokesman for the Mattagami First Nation-Nishnawbe Aski Nation said the group remains opposed to the enactment of a First Nations education act, despite the signing of the joint plan.
"The signing of this historic MOU in no way detracts from our steadfast opposition to any federal legislation with respect to First Nations education," said Deputy Grand Chief Goyce Kakegamic.
"We need education, not legislation, through fair and adequate funding that will ensure that First Nation students receive a quality education on par with students across Canada."
Kakegamic said any such act would amount to a back-door revision of the Indian Act, with the potential to diminish education, not improve it.