The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal’s susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.