Cooper, who moved into the starting lineup last season and led the Chargers with 179 tackles, said in a statement released by the team that he took a stimulant that was recently added to the NFL's list of prohibited substances.
"I regret that I mistakenly took a stimulant that I did not realize at the time was banned by the NFL," Cooper said. "I support the NFL's anti-doping policies, and understand that I must serve a suspension even though the stimulant that I took was not used before any game and was not used to enhance my performance.
"I apologize to the NFL, my team, my coaches and to my fans, and I look forward to continuing to help the Chargers toward our goal of winning the Super Bowl in the upcoming season."
Neither Cooper nor his agent could immediately be reached for further comment.
While at Maine, Cooper admitted to possession of steroids after being found with about 1,000 pills in his duffel bag when the driver of an SUV he was riding in was stopped for speeding in 2002.
Cooper, who pleaded guilty to a misdemeanor drug charge, said at the time that he never took the steroids, but had been planning to use them to bulk up in hopes of making the NFL.
It's the second time since 2006 a Chargers linebacker has been suspended for violating the league's substance abuse policy. Star outside linebacker Shawne Merriman served a four-game suspension in 2006 after testing positive for steroids.
General manager A.J. Smith said the suspension was "very disappointing."
"Coop has embarrassed himself, his family and the Chargers," Smith told The Associated Press. "He made a mistake. Some people learn from their mistakes, others do not. I do believe Stephen Cooper will learn from his and in a positive way. Only time will tell."
Smith said he didn't know what stimulant Cooper tested positive for.
Cooper's suspension begins on Saturday, Aug. 30 following the Chargers' final exhibition game. He is eligible to return to the active roster on Monday, Sept. 29 following the team's Sunday game against the Oakland Raiders.
Cooper can participate in the team's offseason program and in all preseason practices and games.
"Obviously we're disappointed, just as I know Stephen is," coach Norv Turner said in a statement. "Coop made a mistake and now must deal with the consequences. It's unfortunate, but we'll deal with it and move on."