The director-general’s role is the most senior in the Civil Service, overseeing science and higher education policy. Sir John, the former vice-chancellor of Cranfield University, took up the role only in February 2013.
The science and innovation part of his portfolio will be filled by Gareth Davies, executive director and chief economist in the Cabinet Office. The higher education part will be taken over by Philippa Lloyd, who will also remain as director-general for people and strategy at BIS.
The two elements of the role were previously separate, but were united under Sir John’s predecessor, Sir Adrian Smith, who is now vice-chancellor of the University of London.
A BIS spokeswoman confirmed that Sir John would be leaving the department at the end of January.
“Sir John O’Reilly has done an outstanding job as director-general for knowledge and innovation, overseeing a successful 2013 Spending Review and building on the UK’s strengths in research, innovation and higher education,” she said.