Croton planaltoanus, a new species from the Brazilian Cerrado, is described and illustrated here. The morphological relationships of this species are discussed in comparison with C. inaequilobus, an endemic species of the Chapada dos Veadeiros Region, which resembles the new species morphologically. The new species is apparently endemic to the Brazilian Cerrado region, where it grows in “cerrado rupestre” and montane grasslands on rocky soils. The systematic position of C. planaltoanus in relation to the sections of Croton is also discussed.