Smith, 40, also pleaded not guilty to possession of drug paraphernalia and driving with a suspended license. A fifth charge, possessing or selling a controlled substance, was dropped.
Smith did not attend the arraignment at Duval County Courthouse. He was represented in court by his attorney, Hank Coxe, who did not comment on the case after the hearing.
Smith, who played 10 seasons for Jacksonville, was pulled over April 23 on Interstate 95 in Jacksonville for excessive window tint on his 2009 Mercedes Benz, according to the Florida Highway Patrol.
The trooper reported that the inside of the car smelled like burnt marijuana. During a search, the trooper found crack cocaine, marijuana and a business card with powder cocaine residue in the car's center console.
Smith retired from the Jaguars in 2006 after playing from 1995 to 2005. He finished with 862 receptions and 12,287 receiving yards and 67 touchdowns. He was a five-time Pro Bowl selection.
Despite the exceptional stats, Smith's career was not without problems.
In 2001, he had three operations to remove scar tissue from his abdomen. Some questioned whether he would play again, but he caught 112 passes for 1,373 yards -- despite being arrested in November that year for suspicion of drunken driving. Tests later revealed he had cocaine in his system. He vehemently denied using the drug.
He was suspended for the first four games of the 2003 season for violating the league's substance-abuse policy. He then publicly acknowledged an addiction and spent several weeks in rehab.
Smith is represented by Coxe and Brian Coughlin. His next court date is set for June 17.