In 1989, just one year after foundation, the club's name was changed to Vārpa Ilūkste, and they finished the league in the 14th position.

In 1997, after 4 years of silence, the team was reformed as FK Ilūkste and took part in the Latvian First League, finishing in the 9th position.

[1] Before the start of the 2007 Latvian First League season the club was renamed Ilūkste/BJSS to mark their partnership with the local Children and Youth Sports School (Bērnu un jaunatnes sporta skola).

The club withdrew from the championship in mid-season due to financial difficulties, and they were once again relegated to the Latvian Second League.

They started the season playing their home matches in Daugavpils due to the reconstruction of the Ilūkstes pilsētas stadions.