Yoon hurled one-run baseball over 7.1 innings and fanned 10 batters against reigning national champion Kyungsung University in his first 2009 season game as a starter.
However, Yoon was sidelined with injuries for 3 months and finished the season with a 2.36 ERA and 45 strikeouts in 34.1 innings pitched.
He led the national collegiate league in ERA, and was sixth in strikeouts (67) and seventh in wins.
As a senior in 2011, Yoon had another strong collegiate season, posting a 6–2 record and an ERA of 1.38 and fanning 66 strikeouts.
In September 2011, Yoon was called up to the South Korean senior national team for the 2011 Baseball World Cup held in Panama.