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The Apinajé have never left the region they traditionally inhabit, the area of the junction of the Araguaia and Tocantins rivers, the southern border of which was, up until the beginning of the 20th Century, formed by the Mosquito (in the Tocantins watershed) and the São Bento (on the Araguaia) rivers. Presently, the Apinajé Indigenous Land is located in the municipalities of Tocantinópolis, Itaguatins and São Bento, in the extreme north of the State of Tocantins.

The Apinajé Indigenous Land covers an area of 141,904 hectares, and is homologated and registered in the CRI and SPU (Dec. 90969 of 02/14/DOU 02/15/85). The Apinajé, however, are demanding the amplification of the area, and the FUNAI, in 1994, established a work group to identify the indigenous area called Apinajé II; this process since then has been going through bureaucratic channels in the indigenist agency to determine the landholding situation of the region.

From the point of view of the conservation of local ecossystems, the Apinajé Indigenous Area is relatively well preserved, having rapidly recovered from the degradation caused by the presence of more than 600 families of the non-indigenous regional population on their lands up until the demarcation of the area was completed in 1985.

The Apinajé Indigenous Area is directly affected by two dirt roads that are in the process of being built and will probably be asphalted: 1) TO 126: that connects the municipalities of Tocantinópolis and Itaguatins, passing through Maurilândia, cutting a section from north to south of the territory, all along its eastern side; the villages of the Apinajé Indigenous Post (Mariazinha, Botica, Riachinho and Bonito) are located along the side of the road; 2) TO 134: from the municipality of Anjico to the junction of BR 230, continuing on to Tocantinópolis; part this road forms the southern border of the area. This road, which was recently asphalted, passes a few kilometers from the village of São José.

Up to 1999, BR 230, better known as the Trans-Amazon, crossed through the Apinajé territory for approximately 30 kilometers and continued on as the border of its western part. In June, 1997, the IBAMA [Brazilian Ministry of the Environment] interdicted highway construction, in the stretch between Araguatins and Estreito, demanding environmental licensing to continue the construction work. After public hearings and a paralization of the asphalting of the highway by the Apinajé, there was a change in the official routing of the road. From the highway circle of Prata, as is it called, BR 230 goes on to Nazaré, with the name of TO 134, whence it continues on to the municipality of Lagoa de São Bento.