Mr Kirby will take up the Chief Operating Officer roll at Rolls Royce.
He joined HS2 in May 2014, a company set up to oversee the creation of a new multibillion-pound rail link between London, the Midlands and Northern England.
In a statement, Mr Kirby said: "HS2 is not just a highly ambitious project, but also one which will leave a lasting legacy for Britain. It has been, therefore, a huge honour to have been its Chief Executive and to have been involved in creating a leadership team made up of the best talents from this country and elsewhere. I have absolute confidence in their ability to deliver the project and, in doing so, to help transform the way we do things in this country."
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HS2 Chairnan, David Higgins, added: "I am delighted for both Simon and Rolls Royce that he has been appointed to this position. Whilst naturally we will miss his experience and leadership, I also recognise that he is joining a truly great, global company in an industry in which he has previously worked.
"In his two and half years with the company, Simon has used his vast experience to recruit and shape a world class team which over the coming years and decades will turn HS2 into a reality that will be of lasting benefit to this country."
Mr Higgins also revealed the former Chief Executive of Amey, Mel Ewel, had been appointed to HS2's board as Non Executive Director.
"His great experience in the construction industry speaks for itself, as does the huge respect in which he is held," he said.
"As such he will be a great asset to the Board's deliberations as we move to the point of construction."
(LM/CD)
