Downs was born in New York City on October 10, 1913. His father was Lt. Morey Downs, a naval aviator with the U.S. Navy. When he was 8 years old the family moved to San Diego due to his father's transfer. Johnny's mother took him to Hollywood for an audition with the Hal Roach studio. He appeared in a silent film, then was cast as Johnny in the Our Gang series. He was a regular in the series from 1923 until 1927, appearing in 24 episodes.

In 1934 he returned to Hollywood and landed a small part in the musical Babes in Toyland. He found his niche in the "college musical" movies of the late 1930s, starting with College Scandal (1935) and College Holiday (1936). With his boy-next-door good looks, he was often cast as a team captain or a Cheerleader. Other movie musicals followed, ending in 1944 with What a Man!. He had a notable cameo in the 1945 film Rhapsody in Blue where he danced to Robert Alda's piano playing of "Swanee". For the remainder of the 1940s and early 1950s he had a few bit parts in films, including Cruisin' Down the River. He spent most of his time on the stage in summer stock and Broadway, scoring a hit in Are You With It?. Altogether he has almost 100 movie credits to his name.

According to Carleton Carpenter's autobiography, Downs worked as a Choreographer in the theater in the late 1950s on a production called Lock Up Your Daughters. He "did our dances, and they were really foolish. It wasn't choreography; I don't know what it was. I do know it wasn't good, and it became a great source of amusement for all the company-- behind Johnny's back, of course, but we were about a subtle as a bus wreck. It bonded the cast completely together."

He settled in Coronado, California, near San Diego, where he sold real estate and became a respected amateur tennis player. From 1953 to 1968 he hosted a local, after-school kids' television show, The Johnny Downs Show, on Channel 10 (call letters KFSD until 1961; subsequently KOGO). The theme started out as an airport hangar with Downs playing a former World War II pilot, "Johnny Jet". In between reruns of The Little Rascals, Downs entertained and informed his studio audiences and his viewers. After that, it was trains, and he could be seen getting off or on a locomotive at the start and end of a show. As the show changed to feature more Popeye cartoons, his theme changed from being a train Engineer to being a boat captain at the San Diego harbor. Since one of the show's frequent sponsors was a local dairy (Golden Arrow Dairy), Downs was regularly featured as a superimposed miniature Dancer on top of an old-style milk bottle. Children were welcome to come to the KOGO studio and watch the program being broadcast. When each show concluded, Downs would wave to the viewing room and the visitors would go into the studio. He would let kids put on his coat and cap and mimic his opening "Howdy, howdy, howdy! Good to see ya! Good to see ya!" There was briefly a morning show where he invited students to come and compete in math quizzes. During this time he also appeared as the Tin Woodsman in the San Diego Starlight Opera production of "The Wizard Of Oz.

Downs died of cancer on June 6, 1994 in Coronado, California. He is interred in the Holy Cross Cemetery in San Diego. Downs and wife June had five children: Mary, Claudia, John Jr., Mollie and Maureen.