The club's trophy cabinet stayed empty until their centenary year, when in 2006 they lifted both the Corgoň Liga title and the Slovak Cup with the help of 21 goals from the league's joint top scorer Erik Jendrišek.

The team was coached at that time by František Komňacký who in February 2007 went on to SKVO Rostov-on-Don.Corgoň liga: Komňacký v Ružomberku skončil The league win gained them entry into the Champions league second qualifying stage, there they met Swedish side Djurgårdens IF, Ružomberok lost the first leg 1–0 but managed to pull back the deficit to win 3–2 on aggregate.

The next round saw them meet Russian champions CSKA Moscow, the team lost conceding 5 goals without reply.

Over the last period there has been a steady increase of young players leaving Ružomberok after a few years of first-team football and moving on to play football in leagues of a higher standard, mostly Czech First League (Igor Žofčák[1] and Juraj Kucka to Sparta Prague[2] in 2007 and 2009, Maroš Klimpl and Tomáš Oravec[3] to Viktoria Žižkov in 2001 and 2002, Dušan Švento to SK Slavia Prague in 2005,[4] Marián Had to Brno in 2004,[5] Marek Bakoš to Viktoria Plzeň in 2009,[6] and Tomáš Ďubek to Slovan Liberec in 2014[7]), Belgian Pro League (Martin Regáli to K.V.

[9] The top transfer was agreed in 2006 when 24 years old attacking midfielder Marek Sapara moved to Norwegian champion Rosenborg BK for a fee €1.3 million.

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