Allison, 45, was most recently a scout for the Red Sox in 2011-12. Prior to that he spent four years as director of scouting for the D-backs from 2007-10.
Allison fills a vacancy that hadn't been filled since Carmen Fusco was dismissed in September 2010.
"We are excited about the addition of Tom Allison to our organization as Director of Pro Scouting," Mariners general manager Jack Zduriencik said in a statement. "He brings a level of experience with his background as a crosschecker, scouting director, Minor League player and front-office executive. He is a well-rounded individual and his contributions will be an asset to the Seattle Mariners."
Allison spent seven seasons in the Brewers scouting department from 2000-06, working with Zduriencik in Milwaukee, and also has 10 years with the Mets. He played as an infielder and coached in the Mets' farm system from 1990-94.
Allison grew up in Vancouver, Wash., and played baseball at Loyala Marymount University in Los Angeles before earning his degree in Legal Studies at Chapman University in Orange, Calif.