In a letter sent to the Board of Education Tuesday, Kowba announced his retirement would take effect June 30.
Kowba was named the SD Unified district's superintendent on June 29, 2010. Before that, he also served as the district's interim superintendent since September 2009.
In his letter, Kowba cited the board's efforts to work within budget deficits.
"Concurrently, we have been able to maintain a laser focus on academic excellence and not allow the budget woes to distract from our core educational mission. The results speak for themselves," he said.