The separation of rare metals from the ores and commercially available compounds is an important issue due to the need of their high purity in advanced materials and devices. Important examples of two highly important elements that co-exist in the ores are scandium and thorium. Scandium containing ores and consequently also commercially available scandium compounds often contain traces of thorium which is very difficult to separate. We used graphene oxide for the selective sorption of thorium ions from scandium and thorium mixtures originating from the mined ores as well as from commercially available scandium salts. Our results showed that graphene oxide has an extreme affinity towards thorium ions. After the sorption process the graphene oxide contained over 20 wt% of thorium while the amount of scandium sorbed on GO was very low. This phenomenon of high sorption selectivity of graphene oxide can be applied in industry for the purification of various chemicals containing scandium and for separation of thorium containing mixtures. Alternatively, this methodology can be used for preconcentration of thorium from low-grade ores and its further use in the new generation of nuclear reactors.