Werner Rathmayr began his professional career in January 1990 in Innsbruck. At the Junior World Championship in 1990 in Štrbské Pleso , he was world champion in team competition with the Austrian team. He surprisingly won his 4th World Cup competition on the large hill on December 15, 1991 in Sapporo . This was followed by a second place in Oberstdorf as part of the Four Hills Tournament and further top ten placements. He finished the season in second place overall . Also in the following season he made a double victory in Falun on the 5th / 6th. December 1992, two second places in Ruhpolding and Sapporo one and two weeks later and further top ten placements attracted attention. After a serious fall at the World Championships in Falun, Rathmayr was unable to build on past successes. At the beginning of 1995 he finally ended his career in jumping, and at the beginning of 1997 also in ski flying .
After his active career, Rathmayr was the coach of the Austrian B-team in ski jumping. He also gives ski jumping courses for amateurs.
Rathmayr was known for his characteristic jumping style, which was characterized by numerous corrections with his hands and fingers during the flight phase and which earned him the nickname "pianist of the air".