Carlos de Pena is the trainee of Uruguayan side Nacional. He made his debut for the first team on February 20 2013. On June 2 2013 de Pena scored his first goal in the Uruguayan league last matchday.
On September 1 2015 de Pena signed a contract with the Championship side Middlesbrough FC.
On January 31 2017 he went on loan move to Real Oviedo. On July 19 2017 his contract with Middlesbrough was canceled by mutual agreement of the parties.
In 2018 Carlos featured for Nacional again and then became free agent.