The 19,000-seat arena is being built across the street from the LIRR's Atlantic Terminal in Downtown Brooklyn.
"We're going to have to alter Brooklyn service to meet the needs of what will go on at the Barclays Center," Lhota said.
"If a basketball game starts at 7 o'clock at night, it should be over by 9:30, 9:45. We need to be prepared at that time for people to come down, fill up the trains, and then pull another train in."
As part of widespread service cuts throughout MTA operations in 2010, the LIRR eliminated all Brooklyn trains between midnight and 5 a.m.
LIRR president Helena Williams said the agency does not plan to reinstate scheduled overnight service but will add trains as needed, depending on what events are being held at the new arena.
She said it is more likely that concerts, which run later, will require trains after midnight than Nets basketball games.
"It depends on how much they book Barclays [for other events]. Right now I'm going to do it on an event-basis," Williams said. "If in fact they start booking every single night . . . then I'll have to examine, 'OK, do I need to add any trains permanently to the schedule?' "