Abstract This study contributes to the flora of ferns and lycophytes, also referred to as pteridophytes, from the Estação Ecológica Serra Geral do Tocantins (EESGT), which is part of the Jalapão region in Tocantins. Although Jalapão is one of the largest protected areas in the Cerrado vegetation of Northern Brazil, its biodiversity has, thus far, been poorly reported in the literature. Therefore, fieldwork was recently carried out at EESGT in different habitats. Our collections and data from digital repositories included 31 ferns and four lycophyte species belonging to 20 genera of 15 families. Despite occupying only a small fraction of the landscape, forests concentrate most pteridophyte diversity, reinforcing their importance for the conservation of this group within the Cerrado. Eleven species are new records for Tocantins, one is new for Bahia, and one was recently described (Anemia areniticola). In addition to a list of all taxa, we provide illustrations and an identification key to encourage further studies on this often-neglected component of Cerrado flora.