The lawsuit names Perdue's appointee -- Bill Harrison along with the Governor and the State Board of Education as defendants.
Atkinson says she wants to run the state department of public education, but her position doesn't allow that.
"It is not in the best interest of public education for people in the department of public instruction or our students for this situation to linger and fester," Atkinson said.
An audit found that her position is more of an educational ambassador and that she does not run the Department of Public Instruction.
Bill Harrison holds the position that runs the department.
When Perdue appointed Harrison CEO of public schools and chairman of the State Board of Education, Atkinson stood in the background.
"It was uncomfortable for me, but I wanted to show Gov. Perdue support," Atkinson said.
Atkinson also maintains it doesn't make financial sense to have two people do the job one person can do.
Perdue has responded to claims of the accusation that Atkinson is paid $1230,000 a year while sitting idly.
"I don't believe any elected statewide official is a figurehead, and I resent that on behalf of Atkinson and the voters of NC," Perdue said. "June will have a very profound role in working for us and to communicate and to transform public schools and education."
But Atkinson, who was elected to her position, has little to do officially since Perdue hired Harrison.
Ultimately, Atkinson wants lawmakers to change the state constitution to either give the superintendent the power, or eliminate the elected position and make it a position that is appointed by the governor.
A ruling Atkinson's lawsuit is expected by the end of this week.