His comments come at a time when more people are flying to more places, but the number of pilots being trained are unable to keep up with demand.
Demand for air travel is growing so rapidly that 800,000 new pilots are expected to be needed over the next 20 years, according to Boeing's latest forecast.
The biggest need is in the Asia-Pacific region, where an improving economy in China has resulted in more people booking flights. More people are flying in the U.S. too but, at the same time, experienced pilots are reaching the mandatory retirement age of 65 years old.
Speaking to CNBC's Phil LeBeau at the Paris Air Show on Monday, Muilenburg described a global pilot shortage as "one of the biggest challenges we have going forward."
Muilenburg said that, according to Boeing's latest outlook, the market place would climb to $8.7 trillion, up from $8.1 trillion, over the next 10 years. He also estimated the number of new commercial airplanes would rise to 44,000, up from 43,000, over the next two decades.
"If you look at those 44,000 new airplanes over the next 20 years, to go along with that we need about 800,000 new pilots, 750,000 new aviation technicians and so building that talent pipeline for the future is really important," Muilenburg said.
"That's an area where Boeing will be making additional investments."
The U.S.-based airplane manufacturing giant is scrambling to restore confidence in the 737 Max from regulators, customers and the flying public.
The 737 Max has been grounded across the globe since mid-March after a deadly crash involving the jet in Ethiopia. Less than five months earlier, a Boeing Max crashed in Indonesia.
The disasters killed a total of 346 people. Investigators said the jet's MCAS flight control system, which is designed to push the aircraft's nose down to prevent stalling, was involved in the crashes.
Boeing's chief executive said he was not focused on orders for the 737 Max during his time in the French capital, insisting there would be "plenty of opportunities" in the coming months.
Muilenburg said the company had more than 4,000 of the 737 Max aircraft in backlog.
Earlier this month, Muilenburg said that he expects the planes will get a green light to fly again by the end of the year. He declined to provide a more specific timeline when asked on Monday.
Airlines that have purchased the 737 Max, including American Airlines, United Airlines and Southwest Airlines have canceled thousands of flights due to the grounding and have scrambled to meet demand during the peak summer travel season.