Harris, who was with the Indians during the Winter Meetings, will replace Carter Hawkins, who was recently promoted to assistant general manager.
Harris joined the Pirates in February after working with the NFL's Philadelphia Eagles since 2013, serving as then-head coach Chip Kelly's chief of staff. Harris served in the same role with Kelly at the University of Oregon, where he previously spent nearly four years as an associate athletic director.
Switching to different sports isn't necessarily uncommon for executives; former Mets executive Paul DePodesta joined the Cleveland Browns as their chief strategy officer in January.
Cash Kruth is a reporter for MLB.com. Follow him on Twitter at @cashkruth. This story was not subject to the approval of Major League Baseball or its clubs.