A thief stole the control stick from an R train Monday while it was parked underground in southern Brooklyn, the Daily News has learned.

The train was parked just south of the 86th St. station in Fort Hamilton Monday afternoon when a transit worker noticed the lead car was missing the so-called “master controller,” sources told the Daily News.

A master controller — which on an R160 subway car, like those on an R train, consists of a T-shaped handle on the train operator’s right-hand side — controls a subway’s acceleration and braking.

A photograph obtained by The News shows an empty space where the controller should be, with a strand of wiring hanging out into the cab.

All subway trains have a control cab at each end, and sources told The News that the master controller at the other end of the R train was still intact.

The train was parked on what’s called a “layup track” between the 86th St. and 95th St. stations along the Fourth Ave. line — in a section of tracks meant for storing trains overnight or in between rush hours, or for storing damaged subways before they can be moved back to a train yard for repair.

The theft was discovered shortly before 5 p.m. Monday, though it was not immediately clear when it happened.

Sources told The News that police were notified shortly afterward. The affected train remained on the layup track until the late-night hours, when it was moved to Jamaica Yard for repairs.

The theft occurred along a stretch of southern Brooklyn layup track that’s become a hot spot for subway vandals. In May, the same layup track was the site of a joyride broadcast on social media, in which two young transit trespassers threw an R train into reverse going 20 mph.

Neither the NYPD nor the MTA responded to requests for comment.