Besides Calhoun, who will stay in his post through the end of 2024, Boeing announced two other major changes to company management.
Stan Deal, Boeing's head of commercial airlines since 2019, will exit immediately, while the company's chairman, Larry Kellner, a former airline CEO, will depart after the company's annual meeting this spring.
Replacing Deal will be longtime Boeing executive Stephanie Pope, while former Qualcomm CEO Steve Mollenkopf will serve as the new chairman.
The sweeping personnel changes come in the wake of Boeing's near-catastrophic incident in January when a fuselage panel on a Boeing 737 MAX 9 Alaska Airlines jet blew off mid-flight.
Calhoun called the Alaska Airlines incident a "watershed moment" for the company in a letter to employees.
"The eyes of the world are on us, and I know we will come through this moment a better company, building on all the learnings we accumulated as we worked together to rebuild Boeing over the last number of years," Calhoun said.
Shares jumped on the announcement, which follows criticism of Boeing's manufacturing and quality control practices from the Federal Aviation Administration, which had given Boeing 90 days to come up with a plan to address the problem.
Restive clients
Boeing also faced heavy questioning from airlines, who had requested a meeting with the Boeing board in a move seen as a sign of restiveness among the carriers.
The Alaska Airlines incident put Boeing back in the hot seat, a familiar spot after a 20-month grounding of the 737 MAX following fatal crashes in 2018 and 2019.
The company has faced questions following several other potentially dangerous episodes in recent weeks, including an engine fire on a Boeing 747 shortly after takeoff from Florida in January.
Earlier this month, a Boeing 777 jetliner bound for Japan had to make an emergency landing shortly after takeoff from San Francisco when a wheel fell off and plunged into an airport parking lot, damaging several cars.
Last week New Zealand authorities launched an investigation after a Boeing 787 Dreamliner violently lost altitude mid-flight from Sydney to Auckland, injuring some passengers.
In an interview with CNBC, Calhoun described the personnel changes as "all about a clear path to give our best people internally an opportunity to shine in front of the board to demonstrate everything that they can do."
Besides getting a better grip on safety and quality control, Calhoun said the new Boeing CEO will need to "know how to handle a big long-cycle business like ours," including overseeing the company's next airplane, a $50 billion investment.
Formerly head of Boeing Global Services, Pope was promoted to Chief Operating Officer in January. She takes over commercial planes immediately.
With degrees in electrical engineering, Mollenkopf, a Boeing board member since 2020, will lead the process to oversee the next CEO.
Shares of Boeing rose 2.6 percent in early trading.