Gooden, 54, was pulled over in Holmdel, N.J., just before 1 a.m. EDT on June 7, a police spokesperson told the New York Post and New York Times. Police said they found "two small green zip-lock style plastic baggies suspected cocaine" in his car.
He was charged with third-degree possession of a controlled dangerous substance, as well as possession of drug paraphernalia and being under the influence.
Gooden faces three to five years in prison if he is convicted. An initial court date has not yet been set.
Gooden has battled drug and alcohol addictions for over 30 years. He entered rehab in 1987 after testing positive for cocaine during Mets training camp and missed all of the 1995 season for failing another drug test.
Gooden served eight months in jail in 2006 for violating probation when he told his probation officer he had used cocaine.
Gooden was 194-112 from 1984 to 2000. He was named the National League's Cy Young winner in 1985 and won three World Series titles, including one with the Mets in 1986 and two with the rival Yankees in 1996 and 2000.
Gooden threw a no-hitter with the Yankees in 1996. He ended his career with a 3.51 ERA and 2,293 strikeouts in 2800 2/3 innings.