The Grant Agency is administered by a Presidium appointed by the government of the Czech republic. The Presidium is authorized to organize tenders for scientific and research projects and to award grants. The Presidium is assisted in these tasks by Advisory Area Committees set up in five general branches of science; it is also advised by additional Area Subcommittees, i.e. groups of specialists organized according to scientific and technical fields. Together these committes undertake the work of evaluating the grant proposals received.

The work of the GACR is monitored by a Supervisory Board appointed by the Czech Parliament which is independent of the other GACR organs.