Anthony Smith, who has been head of the School of Pharmacy, University of London, for five years, will become vice-provost (education) at UCL from 1 January.
Professor Smith was criticised by some staff over the handling of a strategic options review at the school, which considered whether to merge with either King's College London or UCL, or to remain independent.
In June 2010, members of the academic board passed a motion of no confidence in his leadership but he survived the storm and the school's governing council backed a merger with UCL by 12 votes to eight in May this year.
The result of the vote led to more protests from some, as separate surveys of staff and the academic board had both shown that a majority of respondents were opposed to the change. Professor Smith has maintained that the merger will put the school in a better position to tackle the government's funding reforms and the research excellence framework, partly by removing the overhead costs associated with running a small, independent institution.
He said he had been mindful of concerns that the institution would lose its identity, but that evidence from previous mergers involving UCL was that the school would be able to maintain its world-class reputation. The school, which will shortly begin the search for a new director, is expected formally to become part of UCL on the same day that Professor Smith takes on his new role.
Meanwhile, in a separate development, minutes from the July meeting of UCL's council reveal that it is planning to make the Liberal Democrat peer Lord Clement-Jones of Clapham, currently chair of the school's council, a member of UCL's governing body.