Perdue's office says she is considering an appeal, but Harrison said Wednesday that he'll step down anyway.
"As Chairman of the State Board of Education, I want my focus to be on the 1.4 million students in this state, not on a court case," he said in a statement sent to the media.
Harrison will keep his job as chairman of the State Board of Education.
"Six months ago, Governor Perdue asked me to help her transform North Carolina’s public school system and I will continue to work with her and Superintendent Atkinson to do so. I look forward to providing the leadership as Board Chair to ensure every child has access to the constitutionally-mandated sound, basic education," said Harrison.
Perdue appointed Harrison to the CEO job soon after she took office. The position didn't exist before she created it, but Perdue - a former teacher - said it was necessary to improve accountability and establish a clear line of command in the state Department of Public Instruction. Atkinson said the move relegated her to the role of a powerless ambassador for schools and claimed in a lawsuit that it was unconstitutional.
After the court ruling, Harrison told Eyewitness News that he intended to stay on, and that there was plenty of work for both he and Atkinson. She disagreed, telling Eyewitness News by phone from a conference in Colorado Tuesday that she thought he needed to go.
"We need to make sure that we have a very streamlined administration for public education. And I don't believe that we need to have duplication in administrative responsibilities," she said.
Harrison's salary is $265,000 annually. It wasn't immediately clear what it would be after his retirement from the CEO position.
Governor Perdue said Wednesday that Harrison's decision proves his commitment to education.
"Dr. Harrison’s decision today to devote his time to leading the State Board of Education exemplifies what I’ve known all along – that his real commitment is not to a title or to a paycheck, but to securing a world class education system for our children. During this legal dispute, the focus on our kids has been lost in the courtroom. Dr. Harrison’s move today puts the focus back where it belongs – on the classroom," said Perdue in a statement.
Atkinson said in a statement Wednesday that she respects Harrison and will work with him on the State Board of Education.
"I value all of the contributions that Dr. Bill Harrison has made to public education during his career. I look forward to continuing to work with him as he remains in his role as Chairman of the State Board of Education. We both have our eye on the ultimate prize: ensuring the academic success of every North Carolina public school student," she said.