Defense attorney M. Gerald Schwartzbach entered the plea for the 22-year-old Lynch, who was not present.
"I am embarrassed by my recent arrest and conviction. I deeply regret that I placed myself in this situation," Lynch said in a statement issued later. "I have made mistakes in the past. Although I have learned many lessons over recent years, I obviously had not learned enough."
The Buffalo Bills, in a statement Thursday afternoon, said: "Today we learned of Marshawn's guilty plea to the misdemeanor violation. He has accepted responsibility for his actions and apologized for his mistake. The league is now reviewing the matter under the NFL Personal Conduct Policy."
Lynch was arrested on Feb. 11 after suburban Culver City, Calif., police investigated a parked car without license plates and smelled marijuana when the driver rolled down the window.
Lynch and another man were passengers.
Officers searched the car and found a 9mm semiautomatic handgun inside a backpack in the trunk. Prosecutors said the backpack contained other items belonging to Lynch.
Police said they also found four marijuana cigarettes in the car, but no drug charges were filed.
Lynch pleaded to a misdemeanor charge of having a concealed firearm in a vehicle and was sentenced to 80 hours of community service and three years of probation, said Shiara Davila-Morales, a spokeswoman for the Los Angeles County district attorney's office.
The community service will be performed in Oakland, Calif. He could have faced up to a year in jail.
Lynch also agreed to submit to searches by police at any time, and the gun was destroyed, Davila-Morales said.
Two other misdemeanor gun charges were dismissed, she said.
Schwartzbach said in a brief interview that Lynch could have pleaded no contest but chose to plead guilty.
Lynch's statement expressed apologies to his family, the Bills' organization, teammates, the Buffalo community and commissioner Roger Goodell.
"I have already learned from this recent mistake and am sincerely committed to being a more responsible citizen and better representative of the NFL," he said.
Last June, Lynch pleaded guilty to a traffic violation and admitted driving off after striking a female pedestrian with his car near Buffalo's downtown bar district on May 31.
Lynch, the Bills' first-round draft pick out of California in 2007, had eight touchdowns and rushed for 1,036 yards in the 2008 season. He went to his first Pro Bowl game last month, running for a game-high 48 yards during the AFC's 30-21 loss to the NFC.
Information from The Associated Press was used in this report.