Thomas will be responsible for BBC Studios and BBC Post Production which both sit under the BBC Resources umbrella.
He will report to the chief executive of BBC Worldwide John Smith.
Both Post and Studios were retained by the corporation following an attempted sale earlier this year.
Previous roles for Thomas include director of the BBC North Project, which included transferring 1,600 staff from London to a new broadcast centre in Salford.
Commenting on the appointment, John Smith said: "Mark joins at a crucial time for this business. The industry is changing very fast and BBC Resources will need to change too. Mark has shown both drive and strategic vision in previous leadership roles, and will be a terrific asset to the Resources team.”
Thomas has held a number of positions within the BBC. He was director of BBC consultancy to the Public Broadcasting System in Bosnia in which he devised a new relationship with the regulator, a new funding mechanism and stronger cooperation between the competing public service broadcasters.
Thomas also worked as controller of BBC TV Operations. In that role he brought together the operations as well as the planning and scheduling functions.
He also devised and led the implementation of the genre-based commissioning system as well as helping to streamline the commissioning cycle.
Thomas will start his new job on 4 August 2008.
Mike Southgate, the outgoing BBC Resources chief executive, had been due to leave at the end of May but stayed on board to provide continuity and to ensure a smooth handover. He had been CEO since 2001.
The outside broadcast arm of BBC Resources was sold to SIS in April this year.