Manning, who has 31 touchdown passes and has thrown for 4,016 yards this season, topped the fan balloting with 993,045 votes cast on NFL.com.
Fan balloting was closed Dec. 17.
The fan voting is one-third of the equation in determining the Pro Bowl teams and is combined with voting by the league's players and coaches, who will cast their votes Thursday and Friday.
The Pro Bowl teams will be announced Dec. 26.
Manning was followed in the fans' voting by New England Patriots quarterback Tom Brady (908,099); Houston Texans running back Arian Foster (829,591); Minnesota Vikings running back Adrian Peterson (828,225); and Green Bay Packers quarterback Aaron Rodgers (777,827).
Rounding out the top 10 were Washington Redskins quarterback Robert Griffin III (683,943); Cincinnati Bengals wide receiver A.J. Green (676,607); Patriots tight end Rob Gronkowski (646,273); New Orleans Saints quarterback Drew Brees (578,753); and Baltimore Ravens running back Ray Rice (564,751).
The NFL is the only one of the four major American professional sports leagues to determine its All-Star teams by combining fans', players' and coaches' votes.
The Pro Bowl will be played at Aloha Stadium in Honolulu on Jan. 27, 2013.