The 6-foot-5, 200-pound netminder played the majority of the previous two campaigns with IF Bjorkloven of Sweden's Allsvenskan, posting a 2.34 goals-against average and a .915 save percentage in 47 contests during the 2017-18 season. On March 26, 2018, the Mariestad, Sweden, native signed an amateur tryout contract with the American Hockey League's San Antonio Rampage and went 2-1-0 in four appearances with the club (3.35 GAA, .880 Sv%). Werner recorded a 2.98 goals-against average and a .892 save percentage in 25 outings for Bjorkloven in 2016-17 and joined Farjestad Jr. for the playoffs, appearing in one postseason contest.

Selected by the Avalanche in the fifth round (131st overall) of the 2016 NHL Draft, Werner spent most of the 2014-15 and 2015-16 seasons with Farjestad Jr. He played 30 games with club in 2015-16, finishing 20-10 with a 2.49 goals-against average and a .916 save percentage and had a 2-3 record in five postseason outings, registering a 2.55 goals-against average and .924 save percentage. Werner compiled a 15-13 record in 28 contests during the 2014-15 campaign with a 3.01 goals-against average and a .906 save percentage. He also played in six games in the playoffs, finishing 3-3 (3.36 GAA, .899 Sv%).

Internationally, Werner was selected to represent his country at the 2017 IIHF World Junior Championship but did not play a game during the tournament. He suited up for Sweden's under-18 team at the 2013 and 2014 Ivan Hlinka Memorial Tournaments. Werner appeared in two contests in 2014, posting a 3.39 goals-against average and a .865 save percentage and played in one tournament game in 2013.