Pacific Northwest LNG said Greg Kist plans to return to his home and family in Alberta.
"Under Greg's leadership, the company was formed and continues to work towards a final investment decision this year," Pacific Northwest chairman Dato' Wee Yiaw Hin said in a statement.
"He leaves Pacific NorthWest LNG as a strong company with an excellent management team and a committed, dedicated group of employees."
Progress Energy chief executive Michael Culbert, who also serves as a director of Pacific Northwest LNG, will add the role of acting president of the company.
Progress Energy is owned by Petronas.
Pacific Northwest LNG is one of several groups developing an liquefied natural gas project on the West Coast.
The company said earlier this week that it was reviewing the details of the B.C. government's new tax on liquefied natural gas. The CEO of Petronas had raised concerns that an earlier version of the tax, along with a sluggish regulatory process, had put the economics of the proposed export facility into question.