As a participant in the Intertoto Cup, Marek tied 1–1 the German Bundesliga club VfL Wolfsburg in 2003, but lost away from home the second leg, 0–2, and was eliminated from the tournament. The team finished 7th at the conclusion of the 2003–04 season, 9th at the end of the 2004–05 season, 11th after the 2005–06 season, and 12th at the end of the 2006–07 football season of the Bulgarian premier division, Bulgarian A PFG (out of 16 teams). In 2006–07, Marek secured its place in the Bulgarian top division for the next season with a 1–0 home win over the powerhouse CSKA Sofia.