The beginnings of the Ilukste Lutheran church can be traced back to the 16th century. Selonia was a Lutheran land at that time.
By order of the duke in 1568 a Lutheran church was built in Ilukste, but it had a rather short lifetime. When the landlord of Pilskalne had changed his religion to Catholicism, and the last Lutheran pastor in Ilukste, the count Jānis Zībergs, died, being a Catholic, in 1635 the church was given to Catholics, that was confirmed by the Polish king Władysław IV in perpetuity. After the donation of the church was approved, the Ilukste Lutheran church was added to the Lasu Lutheran church.
The existing church was built between 1861 and 1865. The church was destroyed during the First World War, but was restored in 1928.
The Ilukste Lutheran congregation regained its property in the early 1990s.