On July 31, 2007, Gagné was traded to the Boston Red Sox for pitcher Kason Gabbard and minor league outfielders David Murphy and Engel Beltré. Gagné was expected to serve as a setup man for closer Jonathan Papelbon. Theo Epstein was quoted as saying that "I think the bullpen is already a strength of the club, but acquiring a pitcher the caliber of Éric Gagné only makes it stronger and helps give us what we hope will be a truly dominant bullpen for the remainder of the year."
On December 9, 2007, Gagné reached a preliminary agreement with the Milwaukee Brewers. On December 10, he inked the one-year deal to become their new closer. The one-year deal had a base salary of $10 million, with incentives worth up to an extra $1 million. Gagné went back to wearing the number 38 after wearing 83 in Boston.
On December 13, 2007, Gagné was listed in the Mitchell Report—former Senator George Mitchell's report on the use of performance-enhancing drugs in baseball. Gagné was identified as a user of HGH (Human Growth Hormone). Allegedly, Gagné received the drugs from steroids dealer Kirk Radomski. At first, Radomski said that Gagné obtained them from Dodgers teammate Paul Lo Duca, but then Radomski said in the report that he mailed two shipments of HGH directly to Gagné in 2004. Receipts of FedEx and USPS shipments indicate that Radomski received at least one payment from Gagné and two from Dodgers teammate Lo Duca on behalf of Gagné. Gagné declined to meet with Senator Mitchell to respond to the charges before the report was released.