Rooney has worked as a principal and superintendent.
He says he is most proud of building a performance-based educational system and the "Lindsay Transformational Story."
It has allowed students to learn at their own pace and in different ways.
"I want to say thank you to the Lindsay staff, to the Lindsay school board and to the Lindsay community for giving me the opportunity to serve and be part of this incredible journey to advance the life of Lindsay learners," he said. "You will forever be in my heart and in my mind."
Rooney plans to spend more time with his family, traveling and continuing to work alongside the Lindsay Education Foundation.
His last day as superintendent will be in January.