Huntington, 38, spent 10 years with the Indians. The Pirates made him their 12th general manager in team history Tuesday.
"Neal is extremely intelligent, analytical and driven to succeed," Pirates President Frank Coonelly said. "He shares my vision on how to transform the Pirates into an organization that can consistently compete. Equally important, Neal knows how to implement the changes, systems and philosophies required to accomplish that goal."
The Pirates fired General Manager Dave Littlefield Sept. 12. Brian Graham had served as interim GM. Pittsburgh, with a week left in the regular season, will have its 15th consecutive losing season in 2007.
Huntington became the Indians' assistant general manager in 2001. He also served the team as director of minor league operations and director of player development.