Keyshawn Brown was taken into custody without incident at his home on Hemlock Street on Tuesday night, said police.
He is expected to be arraigned on Wednesday at Brooklyn Criminal Court.
Several photos on Facebook show Brown in subway-related clothing including one with the 'N' train logo.
Brown is accused of putting a subway sign in the path of a C train as it entered the Nostrand Ave. subway station on Thursday. The train hit the object causing an explosion.
No one was injured in the incident but the morning commute was significantly delayed as a result.
Brown was arrested last February after he allegedly hit someone with a metal object.
He faces several charges in connection with the subway prank including criminal mischief, arson and reckless endangerment.