The plea comes after G-Dep walked into the 25th precinct and admitted to shooting John Henkel in October of 1993.
G-Dep said he confessed as part of a drug rehabilitation program, but he did not know his victim had died from the gunshot wounds.
According to his lawyer Anthony Ricco, the not-guilty plea was a procedural step, so that G-Dep's confession to police could be scrutinized, because he was most likely under the influence of drugs at the time admitted to the murder.
His lawyer stated that G-Dep's drug of choice over the years was PCP, a powerful hallucinogenic.
G-Dep, born Trevell Coleman, faces 25 years to life in prison over the murder. The rapper is being held without bail.