Atkinson's post is an elected position, and her lawyer argued the Perdue violated the state constitution by appointing an executive with more power than her.
"What they have attempted to do is subvert the constitutional amendment process," said Robert Orr, a former Supreme Court justice whose law advocacy group filed Atkinson's lawsuit in court this week.
The North Carolina Constitution establishes the superintendent as the chief administrative officer of the state Board of Education, whose voting members largely are appointed by the governor to supervise and administer the public schools. But the constitution also says the duties of the schools superintendent, and other elected executive offices like attorney general and agriculture commissioner, "shall be prescribed by law."
That means the General Assembly can pass laws defining their duties, said Mark Davis, a state attorney representing Perdue and the state school board.
A 1995 law gave the state school board flexibility to shape the superintendent's job. Since then, the power of the post has ebbed and flowed, depending on who held the job. In Atkinson's first term, the board gave most of the day-to-day authority of the schools to a deputy superintendent. Atkinson was elected to a second term in November.
In January, Perdue said she wanted the new board of education chairman also to take the new title of schools chief executive officer, clearly making Perdue responsible for how the public schools educate about 1.5 million students. Former Cumberland County schools superintendent Bill Harrison took both posts in March.
Atkinson said her role has been diminished to ambassador for public education.
Perdue, a former schoolteacher with a master's degree in education, said in January that she wants the responsibility for education but didn't want to spend the time and effort to change the constitution.
But Atkinson's attorney said that in diminishing Atkinson's duties, the governor went too far in her shortcut to the hard work of changing the constitution.
"That is a job not given to the superintendent by statute. It is not a job given to the superintendent by the state board. It is a job given to the superintendent by the voters of this state and it can't be transferred to another," Orr said.
Perdue's office said Friday she plans to appeal Hobgood's ruling. In the meantime, CEO Harrison will answer to Atkinson.
"I am reviewing the court's ruling," said Perdue in a statement. "I look forward to continuing to work with Dr. Harrison and Superintendent Atkinson to achieve our goal of providing a quality education for North Carolina's children."