Munro is the latest high-ranking chief to jump ship and decision comes just a few months after she was awarded a CBE in the Queen’s Birthday Honours List in recognition for services to the transport industry.
In June, former commercial director Beth West said she would be stepping down to join London developer Land Securities as its head of development.
Last year former HS2 CEO Simon Kirby also left to join the Rolls Royce as chief operating officer.
Munro joined HS2 Ltd when it was formed in 2009 as chief executive of HS2 and in 2014 moved on to develop the second phase of the line, linking the West Midlands with Leeds and Manchester.
Before that was a director at the Department for Transport and spent several years as a senior manager in the Department’s railways group, including as client for the High Speed 1 project, leading the arrangements for delivery of the second section from Ebbsfleet to London.
David Higgins, Chairman of HS2 said: “Alison is one of the founding pillars of HS2. She has been with the project almost from its inception, and we would not have managed to get to where we are today without her.
“From building the organisation, through steering the Birmingham to London Hybrid Bill through Parliament, to designing the route to Leeds and Manchester, Alison has been a central figure in the development of the programme. She will be missed and we wish her well in retirement.”