Ruffin made the announcement at Monday's commissioners meeting.
In a letter to the board, Ruffin noted that his decision to retire is family-related. He and his wife plan to relocate to the Charlotte area to care for his in-laws.
Ruffin reflected on numerous successes during his tenure.
"I have a great staff, the best department head leadership that we have ever had in my 13 years, and a wonderful group of employees who really care about what they do," said Ruffin. "They have been my employee family and I have enjoyed being their 'manager'."
A blog reports internal county relationships might have spurred the moved, but others say it was truly on Ruffin's own terms to walk away.
Ruffin said he's proud of the community he's leaving and all that it has accomplished under his leadership.
"I'm not leaving over tension with my Board," said Ruffin. "They've been very good to me. They've been very gracious about this."
Ruffin held similar posts in the Atlanta, Charlotte, and the Raleigh-Durham metropolitan areas during a nearly 36-year span.
The Durham Board of Commissioners will begin a search process for a new county manager immediately.