Michael Conway, an American who co-founded America West Airlines and National Airlines, had one year remaining on his contract, said Shirley Williams, the chairwoman of a new board appointed earlier this week.
"There is a clause in his contract that permits him to leave and he exercised it," she said.
As word of his departure spread late Thursday, some workers protested by walking off the job at the Donald Sangster International Airport in the tourist haven of Montego Bay.
The Jamaican government took over the troubled airline in 2004 and launched a restructuring, but the carrier has continued to eliminate routes and lay off workers as it struggles to turn a profit.
In May, Conway announced Air Jamaica was selling its London-to-Kingston route to Virgin Atlantic as part of a strategy to achieve profitability by 2009.