Dennis Muilenburg will not receive severance or separation payments in connection with his departure.
The charge will result in Boeing's largest-ever quarterly loss and "underlines the magnitude of the crisis" it is facing.
The company shipped a record 202 commercial aircraft in Q3 but its KC-46 military tanker program continues to experience delays.
Greg Smith will take on the additional role of executive vice president of enterprise performance and strategy.
The company ended a tough 2016 on a high note as its focus on lowering costs delivered profits that topped analysts' estimates.
