Janet Holder has been executive vice-president for Western Access since 2011 and head of the team overseeing the pipeline project.
Enbridge said leadership of the Northern Gateway project will continue under John Carruthers, president of Northern Gateway Pipelines.
Carruthers will report to Byron Neiles, senior vice-president of major projects and enterprise safety and operational reliability.
"It's been an extremely rewarding experience, but I have decided now is a good time to take a step back and focus on my family and my personal health," Holder said in a statement.
"I look forward to spending more time with my husband at our family home in Prince George."
Holder joined Enbridge in 1992 and was president of gas distribution from 2008 to 2011.
Enbridge had hoped to have Northern Gateway in service as early as 2018, however that is seen as unlikely as the company continues to look for support from B.C. First Nations along its route from Alberta to the West Coast.
The federal government approved the Northern Gateway project earlier this year, subject to 209 conditions, however Enbridge has suggested that a final decision to break ground will not come any time soon.
Northern Gateway would ship 525,000 barrels per day of diluted oilsands crude from the Edmonton area to Kitimat, B.C., where the oil would be loaded on tankers and shipped to Asia.