The church's history began in 1992, when a group of enthusiasts decided that the city needed a second Catholic church. They sought to reestablish a parish in a rapidly growing new part of the city.
On January 16, 1993, a commission was formed to select a suitable site for the new church. A year later, in June 1994, a cross was consecrated on the site of the future church, symbolizing the beginning of this noble mission.
From the very beginning, the construction process attracted a lot of attention and support. On May 12, 1996, the Bishop of Telšiai Antanas Vaičius celebrated the first Holy Mass above the foundations of the future central altar - it was not only a religious, but also a symbolic moment, marking the project as if with a spiritual blessing. On the same day, the cornerstone of the church, which symbolizes the foundation and strength, was consecrated.
In 2004, the construction of the church was significantly supported by AB “Mažeikių nafta”, which allocated as much as 650,000 litas. Such financial support allowed for a faster implementation of the project and ensured high-quality construction progress.
The church's architecture was led by Henrikas Štaudė, a talented Lithuanian architect whose creative style is characterized by modernity and functionality. Thanks to him, the Mažeikiai St. Francis of Assisi Church became not only a place of prayer, but also an architectural decoration of the city.

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