After his minor league baseball career, McCloughan worked as a regional scout for the Green Bay Packers from 1994 to 1999. He then went on to becoming the college scouting director for the Seattle Seahawks from 2000 to 2004 before joining the San Francisco 49ers in 2005 as the vice president of player personnel. In February 2008, McCloughan was promoted to general manager of the team. In March 2010, the 49ers and McCloughan agreed to a mutual termination of his contract.
Shortly after leaving the 49ers, McCloughan was hired by Seattle Seahawks to be their senior personnel executive. He assisted in the team's drafting of players such as Russell Wilson and Richard Sherman. McCloughan remained in this position until April 2014, when he resigned due to personal matters.