Growing up on a farm in Wilkes County, Johnson, like many of the pioneers of stock car racing, developed his driving skills running moonshine as a young man. He was one of many drivers who easily transferred his moonshine experience to the highly pitched pavement of the NASCAR superspeedways.

In his first full season, he won five races and finished sixth in the 1955 NASCAR Grand National points standings. If NASCAR had a Rookie of the Year at the time, Johnson surely would have won it.

The following year, he took an unscheduled trip to prison in Chillicothe, Ohio after an encounter with federal agents at his father's moonshine still in the Carolina mountains. He served 11 months of a two-year sentence.

Johnson returned to the NASCAR scene in 1958 and picked up where he left of, winning six races. In 1959, he won five more NASCAR Grand National races and was regarded as one of the most capable short-track racers in the business.

His first big win at the Daytona 500 in 1960. It was in practicing for that race that he discovered the concept of "drafting," running close behind another car and taking advantage of its slipstream to gain additional speed. Using that technique he won the race, despite the fact that his car was slower than others in the field.

In 1963 he had a two-lap lead in the World 600 at Charlotte before a spectator threw a bottle onto the track and caused Junior to crash.

He retired in 1966. In his career he claimed 50 victories as a driver, and 11 of these wins were at major speedway races.

Johnson was a master of dirt-track racing. "The two best drivers I've ever competed against on dirt are Junior Johnson and Dick Hutcherson," said two-time NASCAR champion Ned Jarrett.

Johnson is credited with the invention of the bootleg turn.