Cooper became a permanent Major League Baseball umpire beginning in 1999. He worked the Division Series (2003, 2005, 2006, 2008, 2009, 2011, 2012, 2013, 2014, 2019), the League Championship Series (2004, 2015, 2016, 2017), the Major League Baseball Wild Card Game (2015 and 2016, 2017), the 2014 World Series, and the 2005 All-Star Game. Cooper also worked the World Baseball Classic in 2009 and 2013.