The attacks immediately set off a scramble by his agency to prevent the same from happening in the U.S., even as Neffenger, who was flying from Newark for meetings with aviation security European counterparts, spent hours trying to get out of the airport.
Now, U.S. authorities are increasing visible security patrols and random checks outside airports. The agency is also working to increase the use of bomb-sniffing dogs who roam public areas as a way to deter such attacks.
And passengers can see some of the changes, Neffenger told CNN.
"They'll see a visible law enforcement presence in the public transit areas that will be local law enforcement, transit public safety, more explosive-sniffing dogs moving around, perhaps more random checks of the people moving through, random checks of the bags they are carrying," Neffenger said in an interview with CNN.
For years, much of aviation security has focused on improving databases to screen ticketed passengers, to prevent terrorists from sneaking a bomb onto an airliner.
But in Brussels, the terrorists didn't bother buying airline tickets. They targeted areas in the terminal that are lightly protected -- the ultimate so-called soft targets -- to deadly effect.
"There are some tactical things you have do to after Brussels, that is, you have to recognize that public areas of the world are vulnerable by definition," Neffenger said. "And to the extent we can, we know the public areas of airports and transit systems provide at times attractive targets, so we've increased our presence ... and we've activated a lot of that over the last couple of years anyhow."
Neffenger said security in public areas outside the security screening stations has always been a concern.
Some airports such as Los Angeles conduct random checks of cars entering the airport, pulling over taxis to check for bombs. For the TSA, the challenge is that the agency doesn't control security checks away handled by local airport police.
Nine months on the job, Neffenger says the TSA is also working to improve how it screens passengers and secures areas behind the security checkpoints. An inspector general report last year
found glaring screening problems. And then there are headline-grabbing episodes, such as airport workers who allegedly were part of a gun smuggling operation at Atlanta's sprawling airport.
The agency is boosting the frequency of criminal background checks for airport workers who have secured badge access to sensitive areas near aircraft.
The idea, Neffenger said, is to bring the perimeter of security closer to the aircraft to reduce the so-called insider threat. That effort has taken on greater importance in the wake of an apparent terrorist bombing of a Russian airliner, which allegedly was aided by someone working at the airport.
The agency is also working to deploy more dogs to screen for explosives. Neffenger says they're among the most effective ways to sniff out potential bombs.
The dogs are being used to screen passengers who haven't signed up for the TSA's pre-check system, which allows passengers expedited screening if they submit to more intrusive background checks ahead of time.