During his initial tenure with the Orlando Predators, Wagner was a key component in the famous "Miracle Minute", in which he scored two touchdowns, two two-point conversions, recovered an onside kick, and made a key defensive stop, all in the final minute of a 1992 game against the Detroit Drive. He was a 7-time AFL Ironman of the Year award winner, 7 years in a row (1992–1997)
During the AFL's 20th season in 2006, the league named Wagner the league's second greatest player of all time behind Eddie Brown.
On Wednesday, March 28, 2007 after being cut from the Tampa Bay Storm's practice squad, he joined the Daytona Beach Thunder of the WIFL. However, after the Thunder ended their season at 4-10, he rejoined the Predators for the 2007 AFL playoffs. On June, Friday 13th, 2008 during halftime at the Week 16 game vs. New Orleans VooDoo, Barry Wagner officially retired from the AFL.
Wagner finished his career with 991 receptions for 13,363 yards and 265 touchdowns. From 1993 to 1999, Wagner posted seven consecutive 1,000 yard receiving seasons. He had 855 rushing yards for 127 touchdowns. On special teams, Wagner posted 6,279 return yards and nine touchdowns, with four of them coming in 1999. Defensively, Wagner finished his career with 677 tackles, 28 forced fumbles, recovering 14, with 47 interceptions and five defensive scores.
As of the 2011 AFL season, he ranks third in league history in receptions, second in receiving yards behind Damian Harrell, fourth in receiving touchdowns. Wagner is tied for second in all-time tackles and fourth in interceptions.