The Cerrado is one of the richest tropical savannas and is considered a biodiversity “hotspot.” It is estimated that, at the current rate of loss, the ecosystem will disappear by the year 2030. The number of new species being discovered in the Cerrado has increased linearly, especially over the last 50 years. We describe a new species of Cnemidophorus from the Jalapão region, in the northern Cerrado biome, Brazil. Linear discriminant analyses and a naïve Bayesian model indicated that a combination of meristic counts (femoral pores, scales around tail, prefemorals, dorsals, and supralabials) and categorical variables derived from pholidosis and coloration clearly distinguish the new species from its congeners. The new species is apparently parapatric with C. mumbuca, the two species occurring on opposite banks of the Novo River. The two species are ecologically and morphologically similar, sharing a small body size, a fixed clutch size of a single egg, and a small number of femoral pores. The new species is apparently endemic to the Jalapão region, in the northern portion of the Cerrado biome. Its small size and restricted geographic range are consistent with findings from Cerrado anurans that undescribed species tend to be small and have reduced ranges. These results highlight the urgency of biotic surveys in Cerrado in face of its accelerated pace of destruction.