Algebra teacher, Alice Hawley, had also been fired for the same reason in the early 1990s.
Around the same time, in November 1993, former Wingfield High School principal, Bishop Knox, was fired for similar reasons.
He allowed a student to read a prayer over the intercom to the entire school.
The prayer read: "Almighty God, we ask that you bless our parents, teachers and country throughout the day. In your name we pray. Amen."
Knox was reinstated as a principal shortly after being fired. He received national media attention, appeared on talk shows and was scrutinized for his "unconstitutionality" for allowing prayer in school.
When asked if he regretted his decision, his response was: "Well, a man can't regret a right decision, at least I can't. And the decision that I made was the right decision."
Meanwhile, Hawley was also asked to come back to the school after being fired the first time. However, it wasn't until several years later.
Fast forward to 2010, and she was asked to come back the next day.
Several graduates of Franklin High and former students spoke in support of Hawley, but also stressed the need for more prayer in the public school system.
"We need to have prayer in our schools. Whether it's student lead, teacher lead, whatever lead, it needs to be in our schools," said Franklin High graduate, Caleb Lehmann.
Carmen Wilkinson is a former student of Hawley's, in the early 1990s. She attributes her faith to what she learned from Hawley more so than what she learned from church.
"She taught me more about God's word than really I learned in church," said Wilkinson.
The Supreme Court ruled in 1962 that schools do not have the right to enforce prayer upon students.
In Mississippi, state statute says that student voluntary initiated prayer is allowed.
Many current students at Franklin High School say they engage in voluntary prayer all the time.
Student Kristie Wallace says students will pray in the mornings before class and even sometimes during the lunch hour.
Former Hawley students say she always gave her class the option to participate in prayer or not.
Hawley herself says she's never received any objections from her students. Hawley is glad to have her job back, but to her, knows the challenge isn't over.
"The real victory will come when we can go in and freely pray, as we want to, as the children want to," said Hawley. "That's when the real victory comes."