Wagner attended Colony High School in Ontario, California, US. In 2007, he registered 125 tackles (92 solo, 33 assists), including four sacks as a senior. Also played tight end, tallying 37 catches for 595 yards with 11 touchdowns. He received all-CIF Central Division honors as well as all-Mount Baldy League accolades. Earned second-team California Division 2 all-state honors after helping lead the Titans to a CIF division title and was named to the all-San Bernardino County team.
Wagner was considered one of the best linebacker prospects in his class. At the 2012 NFL Draft, Wagner was selected in round 2, pick 47 by the Seattle Seahawks. He is the highest selected player from Utah State since Rulon Jones in 1980. Bobby Wagner finished his rookie season with 140 tackles, 2 sacks, and 3 interceptions. After his rookie year with the Seahawks, he was ranked as the #1 rookie inside linebacker, and second in the position in the entire league, by ProFootballFocus. Wagner finished his second season with 120 tackles, 5 sacks with an interception. Wagner helped lead the Seahawks to a 43-8 win over the Denver Broncos in Super Bowl XLVIII.
In his third season, Wagner had an impressive season with 5 games with more than 10 tackles. Even though he missed 5 games, he was voted into his Pro Bowl and named First Team All-Pro. In just 11 games, Wagner recorded 104 total tackles, 2 sacks, 3 passes defensed and 9 tackles for loss at middle linebacker. For the third straight season, the Seattle Seahawks defense finished #1 in the NFL in points allowed, making Wagner a key starter on the #1 defense every year of his career to this point. For his efforts that season, he received a single MVP vote from Tony Dungy, largely due to the Seahawks allowing 20.4 points per game without Wagner and 6.5 points per game in the six games after he returned from a turf toe injury in the middle of the season. In Super Bowl XLIX, Wagner recorded 12 tackles and an interception in a loss.  He is the current all-time career leader for tackles in Super Bowls with 22.
On August 2, 2015, Wagner agreed to a four-year, $43 million contract extension with the Seahawks.