Jeff Morales announced Friday that he will leave the top post at the controversial rail authority in June.
Morales has seen California's high-speed rail project through a contentious and high-profile period, facing constant criticism from across the political spectrum.
Voters approved nearly $10 billion for the project as part of Proposition 1A in 2008.
The CEO's announcement comes one day after the state sold nearly $1.25 billion in bonds for the $64 billion project, considered a milestone after years of legal delays.
Morales says he believes high-speed rail is in a good position so it's the right time for him to move on to another challenge.