Henson led the orchestra through a 15-month lockout of union musicians that ended Feb. 1. The orchestra said Thursday that Henson is resigning by mutual agreement.
In a statement, Board Chair Gordon Sprenger said Henson helped deliver a musicians contract "that was difficult but necessary."
Henson says he's proud of his accomplishments. Since his appointment in 2007, he has led the orchestra's $110 million fundraising campaign and overseen the renovation of Orchestra Hall.
The musicians say they're looking forward to working with the orchestra's board and future management to move the orchestra forward "in a positive direction."
During the lockout, Finnish conductor Osmo Vanska resigned after a decade as the orchestra's music director.