Marek was one of the ten clubs that took part in the inaugural season of the A Group, the newly formed unified league of Bulgaria, in 1948.

Marek managed to defeat Ferencvárosi TC and obtain a home win against FC Bayern Munich in the UEFA Cup, who had been crowned European champions just two seasons before that.

The people of Dupnitsa watched football being played for the first time by foreign troops stationed in the city during World War I.

In 1947, Slavia, Levski, ZHSK, and Athletic decided to merge into one club, which was named Marek, after the nickname of Stanke Dimitrov, a local hero of the Bulgarian Communist Party.

That season, the club led the league for several rounds and at the end the team fought tooth and nail with Slavia Sofia for the third place in the table.

Marek won the decisive game against Slavia in Dupnitsa by the score of 1:0, finishing 3rd and earning an entry into the 1977–78 UEFA Cup.

The return leg in Scotland was tied 0–0 until late in the game, when substitute Gordon Strachan scored a goal and led his team to a 3–0 victory.

The following season Marek once again competed in the Intertoto Cup-against Stuttgarter Kickers (0–1, 0–2), Viking (1–2, 0–3), and Willem II (0–1, 1–4) and finished last in its group.

The town of Dupnitsa was known as the "city on wheels", because thousands of loyal Marek fans would follow the team at away games to remote parts of Bulgaria.

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.

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.

The Bulgarian Football Federation denied Marek the license to compete in B Group for the 2010–11 season due to the team's financial debts.

Thus, the club had to start over and compete at the lowest level of Bulgarian football, in the regional amateur league, Zona Rila.

During the 2012–13 season, Marek finished first in the Southwest V AFG and earned automatic promotion to the Bulgarian Second Division, B PFG Marek surprised its numerous fans with a fantastic 2013–14 season in the Second Division, dominating its opponents and securing promotion to A PFG with four games to go, this returning to the top level after a six-year absence.

After the conclusion of the 2014–2015 season, Marek did not receive a professional license from the Bulgarian Football Federation due to unpaid financial obligations to government institutions, and the team was relegated to the amateur divisions.

Marek, however, managed to equalize in the 83th minute, when a defensive error enabled Aleksandar Bliznakov to chip the goalie and put the ball in the net.