Gilbert was born on April 28, 1967. He is the adopted son of actors Barbara Cowen (née Barbara Crane) and Paul Gilbert and the adopted brother of Melissa Gilbert, who played Laura Ingalls Wilder on Little House on the Prairie, and Actress Sara Gilbert.

Gilbert is best known for his performance as Willie Oleson on the NBC TV series, Little House on the Prairie, from 1974 to 1983. He is also one of only six actors on Little House on the Prairie to appear throughout the entire series, along with Melissa Gilbert, Katherine MacGregor, Richard Bull, Kevin Hagen, and Dabbs Greer. In 1979, Gilbert was in the made-for-television movie The Little House Years also as Willie Oleson. Also in 1979, he was in the made-for-TV-Movie The Miracle Worker as Jimmy. He was in two out of the three made-for-television movies based on "Little House on the Prairie" series of books (Little House: Look Back to Yesterday and Little House: The Last Farewell).

Barbara divorced Paul Gilbert, who died in 1976. In Melissa Gilbert's autobiography, Prairie Tale, it is revealed that due to his suffering from constant pain, he took his own life. Barbara then married Harold Abeles, and together they had Sara Abeles, who changed her name to Sara Gilbert, even though she has no blood relation to Melissa and Jonathan's adopted father, who died one year and two weeks after she was born. In Gilbert's autobiography, she writes that when Jonathan was in his early 20s, he moved away from California and she has had no relationship with him since then, for reasons supposedly unknown to her. She writes that he is a stockbroker living in New York City.