JACKSONVILLE, Fla., Dec. 8— LeeRoy Yarbrough, stock car racing's top driver in 1969, died Friday at University Hospital from internal bleeding in the brain. He was 46 years old.

He had been taken to the hospital Thursday night from Macclenny Hospital, a mental institution at which he was under treatment for what had been diagnosed as ''chronic brain syndrome.'' His brother-in-law, Bob Motel of Jacksonville, said that Mr. Yarbrough injured his head at Macclenny Thursday when he fell after suffering a seizure.

Mr. Yarbrough won $188,609, then a record, on the Grand National stock car racing circuit in 1969, but he spent most of the last four years of his life in mental institutions after being charged with attempted first-degree murder. He was accused of trying to strangle his 65-year-old mother on the evening of Feb. 13, 1980.

'Part of New Breed'

''He was quite a competitor and he had a lot of talent,'' a leading driver, Cale Yarborough, said from his Timmonsville, S.C., home. ''He and I were part of what was known back then as the 'new breed.' We were kind of the second generation of Nascar, so to speak.'' Nascar is the National Association for Stock Car Auto Racing.

During his career, Mr. Yarbrough won the Daytona 500 and the Firecracker 400 at Daytona, the World 600 at Charlotte, the Southern 500 at Darlington, S.C., and the Dixie 500 at Atlanta. His total winnings were more than $450,000.

He was involved in severe crashes at the Texas International Speedway in 1970 and at the Indianapolis Speedway in 1971, and he also nearly died from a case of Rocky Mountain spotted fever.

'Returned to Racing'

He made a comeback in 1972, finishing in the top 10 in nearly every race he entered, but he left the circuit in 1973 to work for a construction company in Jacksonville owned by relatives.

Mr. Yarbrough was committed to the Florida State Hospital at Chattahoochee by Judge Hudson Oliff of Jacksonville on March 7, 1980, after he was tried for attempted first-degree murder of his mother and battery to a law-enforcement officer.

His mother, Minnie Yarbrough, testified that he had walked up to her and started strangling her for no reason. Judge Oliff ruled that Mr. Yarbrough was not guilty of attempted murder because he was unable to distinguish right from wrong at the time of the incident.

In addition to his former wife, Gloria Sapp, Mr. Yarbrough is survived by two children, LeeRoy Glenn and Nicole, four sisters and a brother. His mother died last year of causes unrelated to the strangling incident.