An intruder sneaked into a Bronx NYPD station house Wednesday night — and was caught in the act inside the commanding officer’s room, cops and police sources said. 

Carlos Luciano, 28, entered through a first-floor window that was partially open at the 52nd Precinct’s headquarters on Webster Avenue near the Moshulu Parkway around 10 p.m. Wednesday, police said. 

Cops spotted him inside Deputy Inspector Jeremy Scheublin’s office, according to police sources.

Upon being discovered, Luciano took off running through the station house before being nabbed on the first floor, the sources said. 

He was arrested without incident and charged with burglary, criminal trespass and criminal mischief, cops said. 

His motive was unclear Thursday.

Luciano, who lives about a half-mile from the station house, has no prior arrests, police said.