Harbaugh, who wrapped up his first season as a head coach with a 13-3 regular season mark and the NFC West title, got 45 votes from a national media panel. Green Bay's Mike McCarthy got three votes and Denver's John Fox the other two.
The 48-year-old Harbaugh is the third 49er to receive the top coaching honor. Bill Walsh won the award in 1981 and Dick Nolan in 1970.
Harbaugh led the 49ers to their first playoff berth since 2002. The 49ers earned a dramatic 36-32 win over New Orleans in the divisional round of the playoffs before falling to the New York Giants in overtime in the NFC title game.