Lyons is understood to be moving on to take a new role in the private sector.
He started at HS2 in 2014 as a programme director on the Birmingham stations programme.
He was later promoted to client director before taking then being promoted to the key post of civils delivery director 18 months ago, reporting directly to CEO Mark Thurston.
Before HS2, Lyons worked at Network Rail over 11 years delivering complex projects including rail infrastructure for London 2012 and East Coast Mainline enhancements.
He will be replaced by David Speight, currently client project director for HS2 Area North HS2 Area North
Speight will be supported by Jackie Roe, who has recently joined the project in the role of delivery services director after working at Hinkley Point C for Jacobs.
