He started playing football with USK Anif, a team from a suburb of Salzburg. In 2002 he went to Austria Salzburg, and 2005, after the club was bought by Red Bull, he played with F.C. Red Bull Salzburg.In 2009 he played for the second team of Red Bull Salzburg, Red Bull Juniors. He signed with FC Red Bull Salzburg in 2010. 2011 he played on loan for SV Ried.
Since 2008 Marco Meilinger played for Austria in different youth teams. In 2010 he played with the U 19 team in the European Championship in France and is qualified with the team for the U 20 World championship in 2011.