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It is believed that the first church was built in 1413–1416 under the care of Vytautas the Great, in the same place where the wooden Varniai Church of St. Alexander now stands. The church was consecrated in 1417 and named after St. Alexander (martyr and bishop of Cappadocia and Jerusalem), because this was the Christian name of Vytautas the Great. It is likely among the oldest churches in Žemaitija (Samogitia).


Saušilis village was gifted to the parish church in 1524. The later church was built in 1764.


This is the fourth church in this area built over the past 500 years. Its current image dates back to 1779. The architectural value of the church is an example of the late Lithuanian Baroque period and of wooden folk architecture. After World War II, the church was closed down and barbarically devastated by the Soviet government.


After the bishop of Varniai was transferred, the Church of St. Alexander became the parish church of Old Varniai in 1864. It included Catholics who lived on the right side of Varnelė. The church was converted into a warehouse and later a store in 1949. In 1991, it was returned back to the Catholics and restored.