Roger Quarles, hired only in July, quit the agency earlier this week.
Quarles had been charged with addressing educator complaints about SchoolNet, a program funded largely by the J.A. and Kathryn Albertson Foundation.
After quitting Tuesday, Quarles is returning to a program at Boise State University also funded by the Albertson Foundation.
Superintendent of Public Instruction Tom Luna says Quarles is quitting because he came aboard last year only on the assumption that Luna would be running for re-election.
Luna announced this week he won't run.
Quarles, who just got back from an education conference in London, wasn't immediately available for comment.
Quarles had been paid $120,000 annually in his state post.