The 1st church was built in 1613 or 1630. Owner of Pakruojis Manor at that time Jonas Zabiela, rebuilt a burnt wooden church in 1750. It was made with a cross-plan, 2 chapels and had 6 altars. From his estate, Mr Zabiela donated 3000 Polish golds to the church. In 19th century there was a parish school. As early as 1873 it was asked the permission to build a new church. However, the permission was granted only in 1885. The present brick church was built with Pastor St. Tomkevicius' concern in 1887. The owners of Pakruojis Manor Ropai gave building materials. In 1890 the church was consecrated by Bishop Mecislovas Paliulionis.
Jonas Garalevicius. The organ master, built the organs for Pakruojis church at the beginning of the XX century (up till 1904). This is evidenced by the branded porcelain emblem with the inscription "Jan Garalewicz / Kowno" in the cutter of the instrument.
In 1908, departments of the Sun Society and the Lithuanian Catholic Sober Society were established. During the land reform of 1922, 8 hectares if land were allocated to the church. During the year 1933-1950, the pastor of Pakruojis was writer Mikalojus Seizys – Dagilelis (born 1874 – 1950), (buried in the churchyard). In 1934 he repaired and painted the church and in 1974 wrote a historical outline of Pakruojis parish.
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