Wagner again attended the Kings training camp prior to the 2016 season but was returned to the Pats on October 1, 2016. The 2016–17 season was another breakout season for Wagner, as he set new career highs in goals and assists. That season, the Pats qualified for the WHL playoffs. Wagner scored a goal in Game 6 of the Eastern Conference Championships against the Lethbridge Hurricanes to help push the Pats to the WHL Championship round for the first time since 1984. He ended the playoffs with 21 points in 22 games as the Pats ended up losing the WHL Championship Finals series to the Seattle Thunderbirds 4–2. As a result of his breakout season, Wagner was selected to attend the Canadian National Junior Team camp prior to the 2017 World Junior Ice Hockey Championships but he failed to make the final roster.