They were upset after the school board banned the prayer last month.
"I'm disappointed ultimately in my superior adults and officials," said senior Jessica Woodburn. "I wish there would've been a little bit more time to bring it to the public and consult, and get our opinion."
The American Civil Liberties Union in North Carolina said prayer in public schools violates the separation of church and state. The civil liberties group said they responded after a Franklinton High School student, who isn't a Christian, complained after a prayer was said at a recent awards ceremony.
"They just wanted to be able to attend their commencement without feeling like an outcast," said the N.C. ACLU's Chris Books.
People at Friday's protest said the school board's decision is wrong.
"One person choosing not to [pray] and making a complaint should not make it so that entire 2012 class of three high schools cannot have it as part of their ceremony," said Franklin County resident Jeremy Neal.
Some students plan to hold their own prayer service before graduation Saturday morning.