After pursuing a career in nursing, Pehl realized that she had made a "major bad career choice" and began pursuing a career in comedy.
Growing up in a family of five siblings in Circle Pines provided Pehl with plenty of comedy fodder. She performed standup all around the Midwest from 1987 through 1991. She also worked for the Norrell Temporary Agency, where she earned the title of Temp of the Month for March 1990. She has been featured on VH-1's "Stand-Up Spotlight" and A & E's "Comedy on the Road."
In February 1992, Pehl joined the MST3K writing team after meeting Mike Nelson and Paul Chaplin on the comedy circuit in Minneapolis. She was drawn to the series partly because of her perverse fascination with really bad movies and partly because of the "ineptitude of the people who make them." She appeared as several minor characters, including Jan in the Pan, as well as providing the voice for the shipboard computer Magic Voice. After Frank Conniff left the show, Pehl joined the cast permanently as Pearl, mother to Trace Beaulieu's Dr. Clayton Forrester.
After MST3K was cancelled, Pehl produced comedy segments for National Public Radio.
Pehl has stated that she is a Catholic, and has written for the Catholic Digest, including an article about a priest who works in a circus.
In 2007, Mary Jo joined Mike Nelson in a RiffTrax for the film Glitter. Mary Jo has since become a regular performer for RiffTrax, often working with her former MST3K co-star Bridget Nelson. They have provided new audio jokes for some films previously used on Mystery Science Theater 3000, but have not yet used any of the films from Cinematic Titanic.
In 2016, Mary Jo appeared (along with Joel, Frank, and Trace) at the RiffTrax Mystery Science Theater 3000 Reunion Show. In 2017, she reprised the role of Pearl Forrester in several episodes of the Kickstarter-backed revival of MST3K that was released by Netflix. She was the only Cinematic Titanic cast member (other than Joel) to appear in Season 11 of the revived MST3K. She did not appear in Season 12.
- During the RiffTrax for Sherlock Holmes in Terror by Night, Mary Jo says "I still have my chair from Cinematic Titanic".
- Mary Jo Pehl on Twitter