TSA Spokesperson Mark Howell said the handgun was loaded with seven rounds of ammunition when it was discovered in the Southwest employee's carry-on bag. The TSA said it alerted local law enforcement who confiscated the gun and arrested the man.
The pilot did not have the authorization to carry a firearm, according to Jeff Lea, an airport spokesperson.
It's unclear if the man is facing any criminal charges.
Howell said people who bring firearms to a checkpoint can also face civil penalties.
"We are aware of a situation involving a Southwest Pilot at St. Louis Airport. We are currently working alongside the appropriate authorities to gather more information. We have no further information to share at this time," Southwest Airlines said in a statement.
The pilot was said to be scheduled to fly on flight 1106 to Las Vegas.
Southwest Airlines did not respond to ABC News' question about the status of the flight.
This is the 46th firearm discovered at security checkpoints by TSA officers at the St. Louis airport in 2017, according to Howell. A total of 31 firearms were found there in 2016, the TSA said.
TSA statistics indicate a 28 percent increase in firearm discoveries at nationwide TSA checkpoints since 2015.
This is a developing story. Check back for updates.