Penner was born on November 6, 1946, in Winnipeg, Manitoba, to Lydia Agathe Penner (née Winters, 1913–2005) and Edward W. Penner of Winkler, Manitoba. By the age of four, he had begun making up songs while travelling on the bus with his mother. He taught himself how to play the guitar when he was in grade school, and performed in school choirs and pageants. Through his experiences with his sister Susan, who has Down syndrome, he recognized the therapeutic value of music.
Penner received his high school diploma at Kelvin High School, where he took lead roles in the Gilbert and Sullivan operettas. After graduating from the University of Winnipeg with a Bachelor of Arts degree in economics and psychology, he spent time working with mentally and physically disabled children, using music to comfort and entertain.
By 1972, Penner was a full-time professional musician, performing folk music songs in Winnipeg. In the mid-70s, Penner performed in a number of groups, most notably the folk music group Kornstock, along with Al Simmons, Bob King, both of whom also became well-known children's entertainers, and drummer Mike Klym.

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