An NYPD cop who is suing the department for orchestrating an alleged campaign of revenge against him was arrested Tuesday, police said.

Officer Joseph Stokes and his partner were arraigned Tuesday for separate thefts conducted during an “integrity test” conducted by the NYPD’s Internal Affairs Bureau, officials said.

Stokes took “stash cans” containing $4,800 from an undercover cop posing as a drunk driver and later hid the cash under his car, unreported, parked in the 7th Precinct parking lot, prosecutors allege in their complaint.

Stokes was stung while stopping the undercover officer at Stanton and Orchard streets on the Lower East Side around 1:45 a.m. back on Oct. 29, according to the complaint.

He allegedly found the first wad of $2,100 in a stash can disguise as a can of fruit punch in the vehicle. When the undercover cop told Stokes there were more cans, Stokes told him the money was gone because he threw the cans in a passing garbage truck, the complaint said.

But Stokes was later allegedly caught on precinct security cameras stashing the cans of cash under his car.

Stokes pleaded not guilty Tuesday to grand larceny in the third degree and one count of official misconduct.

Wearing a red puffy jacket with brown fur lining, Stokes looked down and sketched on a pad during the entire time Judge Felica Mennin spoke to him.

Stokes declined to comment as he left the courtroom. His partner, Jose Arecena, 35, turned himself in and was separately indicted on charges of petit larceny and official misconduct.

Stokes is due back in court on March 31.

Stokes previously told the Post the department had targeted for retaliation after pulling over a sports car at 5 a.m. on April 19, 2018. He alleged that the driver threatened him, saying “I’m going to make you f–king pay!” and flashed phone photos of himself with top police brass, including then-Commissioner James O’Neill.

Stokes, an 8 1/2-year veteran of the force who raked in $124,735 in pay last year, charged in legal papers that after the incident the NYPD orchestrated a campaign of revenge against him, ­including a harrowing Internal Affairs sting, a demotion and the leaking of false accusations that he was a dirty cop. He claimed it was all done because he arrested a well-connected drunk.

“I lost the love for this job after seeing how dirty they are,” Stokes, 40, told The Post.