Hoyer, 35, has worked in Boston's front office under Theo Epstein. Hoyer has interviewed with other teams for GM jobs in the past.
Jeff Moorad, who became CEO and part-owner of the Padres earlier this year, informed Kevin Towers on the final weekend of the regular season that he would not continue as the team's general manager. Towers had been San Diego's GM since 1995.
The Padres have interviewed Kim Ng, the assistant GM of the Dodgers, as well as others, in their search for a replacement for Towers.
Buster Olney is a senior writer for ESPN The Magazine.