It changed its name in 2002 after former Belgian First Division club K.S.C. Eendracht Aalst had gone into liquidation. So they could not get the license and the new team began at the third division level. They played the next two seasons in second division (2003–2005) and are now back to the third division and they are at the 3rd place. While the 2004–05 championship was over, the club needed to know if first division side F.C. Brussels and second division side R.E. Virton were to receive the professional football license to know where they would play next season. Indeed, while 17th K. Patro Maasmechelen had no license, they were obviously relegated. So if one of the two submentionned clubs were refused the license, Aalst would have had played the third division playoffs while if they were both refused the license, Aalst would have remained in second division. Finally, both clubs did receive it so the team was relegated. In 2011, the name of the team got changed back to S.C. Eendracht Aalst. They've also requested to change the name back to the former K.S.C. Eendracht Aalst, which will be possible in 2012, if they receive good advice from the Royal Belgian Football Association (RBFA).
During World War I, citizens from Aalst played football matches to raise money for prisoners of war. In 1919 Sport-Club Eendracht Aalst became an official football team. After some friendly games in 1923, SC Eendracht Aalst joined the regional competition. They quickly moved their way up through the regional divisions and after moving the stadion to the current location in 1928, the team made it into the national competition in 1932. Only seven years later, in 1939, Aalst already promoted to the Eredivision (the current Belgian Pro League). Due to the second World War competition was not played for two years, so it wasn't until 1942 Aalst finished its first season in the Eredivision. In 1946 the chairman died and it was decided to rename the stadion to honour him, from then on it was called the Pierre Cornelisstadion. That year was the beginning of a very dark period for Eendracht Aalst. Due to changes in the competition-format, they were forced to relegate. After this they played in the lower division for more than 30 years. In 1960 they managed to get back into the Eredivision, but in 1962 they ended last and relegated again. In 1965, after a bribing-affaire, Aalst was even sent to the lowest national division. In 1977 they made it back into the second division, with Paul Van Himst in the team. In 1994 the team finally joined the first division again. Jan Ceulemans (manager), Godwin Okpara and Gilles De Bilde were some of the most important factors towards success. In 1995 a new climax was reached when they were allowed to enter the European competition and even survived the first round against Levski Sofia.