McNerney, 55, formerly ran General Electric's jet engine division, and is credited with turning around 3M following his appointment there in 2001.
The world's second largest maker of commercial jets is showing a quick turnaround following a pair of highly publicized scandals.
Orders are up for aircraft as passengers return to the skies following the post 9-11 depression. And In 2008, Boeing will debut for commercial use its 787 Dreamliner plane, made of a special composite said to be lighter and more cost-effective than any other large passenger aircraft.
Boeing's previous CEO, Harry Stonecipher, left in March after admitting to an affair with a colleague. Former chief financial officer Mike Sears was jailed after Boeing was found to have made illegal arrangements with a top Pentagon procurement official who later came to work for the company.
Interim CEO James Bell will remain chief financial officer, Boeing said.