McNerney, who formerly ran General Electric Co.'s jet engine division, will succeed Harry Stonecipher (search), who was ousted as Boeing's CEO in March after he admitted to having an affair with a female Boeing executive.
Shares of Chicago-based Boeing (BA) rose 3.6 percent in premarket trading on the Inet electronic brokerage system.
Boeing Chief Financial Officer James Bell (search) had held the CEO post on an interim basis, but he had never been officially in contention for the job, Boeing has said.
Bell will stay on in the CFO job, Boeing said.
McNerney, 55, had been seen as a top candidate for the CEO post from the time the position became vacant, but had repeatedly denied interest.
With the appointment of an outsider, Boeing passed over two top internal candidates, Alan Mulally, head of the company's booming commercial jet business, and James Albaugh, who leads its defense unit.
Both men were on a short list of five or six candidates for the job, Boeing Chairman Lew Platt said during a news conference at the Paris Air Show earlier this month.
Platt will now become lead director at Boeing, the company said.