As provost, Professor Stirling, currently head of the department of physics at the University of Cambridge, will be charged with advancing and delivering the college's "core academic mission", including education and research.
In a US-style structure, he will report to the "president and rector", who has oversight of the whole institution and a greater emphasis on the college's external affairs both in the UK and overseas.
The college is still looking for a replacement for current president and rector, Sir Keith O'Nions, who has filled the role since January 2010 and retires at the end of 2013.
Professor Stirling, formerly pro vice-chancellor for research at Durham University, will take up his position by the beginning of August 2013.
Announcing the appointment, Sir Keith said the theoretical particle physicist was "an individual who has an outstanding scientific mind as well as a track record of leadership in universities, and of service to the national academic community".
Professor Stirling, who has previously worked at the University of Washington in the US and in Switzerland at the European Organization for Nuclear Research, Cern, added that he had "admired Imperial from afar for many years" and believed strongly in what the institution valued.
"To me that means excellence in scholarship - both teaching and research - and excellence in innovation and taking our knowledge outwards to address big societal challenges," he said.
Professor Stirling joined Cambridge in 2008 as the Jacksonian professor of natural philosophy in the Cavendish Laboratory, before becoming head of the department of physics in 2011.
He is also a member of the council of the Science and Technology Facilities Council and the Higher Education Funding Council for England's Research and Innovation Strategic Advisory Committee.
Announcing the change of leadership structure in April, Baroness Manningham-Buller of Northampton, chair of Imperial's council, said the move was about placing more emphasis on strengthening external relationships.
"We need to promote more assiduously Imperial's reputation, to knit together our extensive network of alumni, to raise funds to secure the future, to cultivate our ability to influence and to work in partnership with governments and other institutions," she said.
Professor Stirling's appointment is the second major leadership role at a London institution to be announced this week after Michael Arthur was revealed on 10 December as the next provost of University College London.