The unidentified suspect will be charged with burglary in the 1 a.m. break-in, police said.
Police said the suspect suffered minor injuries. The Los Angeles Times and gossip Web site TMZ reported the suspect was hospitalized after LL Cool J broke his nose and jaw.
The Times quoted police sources as saying the two men had a "knock-down, drag-out" fight.
Police described the suspect as a transient and did not immediately say if he had a criminal record.
"LL Cool J, and his family, are safe and thank everyone for their thoughts and concern," a spokesman said in a statement. "As a father, husband and citizen, he is committed to keeping his family safe and is cooperating with authorities on this private matter."
LL Cool J told police he had been upstairs in his home in Los Angeles' affluent Studio City district when he heard noise coming from the kitchen area. He said when he went down to see what was happening, the suspect came at him, leading to the fight.
Detectives were waiting to interview the suspect.
LL Cool J -- who was born James Todd Smith and whose professional name stands for Ladies Love Cool James -- plays the role of former U.S. Navy SEAL Senior Field Agent Sam Hanna on the CBS police procedural drama series "NCIS: Los Angeles."
Among his hip-hop hits is "Mama Said Knock You Out," from his album of the same name, released in 1991.