Robert Hughes, wrongfully incarcerated at age 16, had turned to his older brother, Donald, who helped him escape in 1964.
The men, still close and living in neighboring apartments, said they chronicled their experiences in a copyrighted manuscript and had an agent pitch it to producers.
They now claim News Corp.'s Fox Broadcasting Co. and others hijacked it.
"It's a classic case of the rich trampling on the poor," Donald Hughes, 63, told The Associated Press.
In a federal lawsuit filed last week, the Hughes brothers claimed Fox was sent their manuscript in 2001 and rejected it before starting to air the weekly drama "Prison Break," about a man who helps spring his wrongly convicted brother from prison.
The show is in its second season.
Their federal copyright infringement case, filed in U.S. District Court in Missouri, seeks unspecified damages and other costs from Fox and the show's executive producer and creator, Paul Scheuring.
Fox Broadcasting Co. spokesman Scott Grogin said the company had not seen the lawsuit and had no comment. Chris Alexander, spokesman for 20th Century Fox TV, the series producer, and Scheuring, its creator, said it's their policy not to comment on pending litigation.
Robert Hughes said he was wrongfully held in juvenile detention in 1964 after his mother, who suffered from paranoid delusions, told authorities he had threatened her with an ice pick. She later recanted, but he was ordered to serve time until he was 21.
Donald Hughes, then 20, planned an escape and sprang his younger brother. For the next four years, the brothers were fugitives, traveling the U.S., working jobs when they could and dodging authorities.
They were exonerated in 1968 after The Kansas City Star published a story about their ordeal.