Chair Marcella Szel said the board had been looking at public confidence for some time and decided it was time to make a change.
Szel said TransLink needed needed stronger leadership heading into a funding plebiscite next month, asking Metro Vancouver residents to add half a percentage point to the provincial sales tax to fund transportation improvements.
Recent polls have shown the "Yes" side softening considerably.
Jarvis was criticized last year for claiming more than $83,000 in bonuses. Despite his resignation, Szel announced Jarvis would continue to stay on as an adviser and collect his full salary until his contract expires in 2016.
TransLink's ability to manage its large budget has come under fire in recent months in the wake of several system-wide SkyTrain shutdowns that caused commuter chaos ending in an independent review that recommended $71 million in improvements to reduce delays and improve communications.
Concerns over TransLink leadership
B.C. Transportation Minister Todd Stone agreed with Jarvis's departure and said TransLink needed a change at the top.
Stone said it was increasingly apparent over the last number of weeks there were concerns about TransLink's leadership.
He said Jarvis's departure should sent a strong message that TransLink is under new management heading into a referendum.
Jarvis's duties will be assumed by interim CEO Doug Allen, who will also participate in the hunt for a replacement.
Szel admits she's not happy to be paying two CEOs' salaries. Under the arrangement, Allen will make $35,000 a month.
Szel says she will meet with the Metro Vancouver Mayor's Council on Thursday morning.