The church was founded in 1625 by the Głuskis of the Ciołek coat of arms, the then owners of the village. The church was built as a limestone church on a brick foundation. It was probably the order's fourth church. It was inaugurated in 1638, but work on it may have taken even longer.
After the fire of 1720, the church was repaired, and in 1723 a rosary chapel, founded by Michał and Franciszek Polanowski, was added to the north side of the church. In 1748 the church was in poor condition (after another fire in 1740), it was repaired and rededicated in 1781. Another renovation of the church was carried out in 1806, and in 1833 it was destroyed by a flood.
In 1876 the church was enlarged to the west (it was extended by three bays and the nave was raised), received a brick chancel and a new facade. The wooden floor was replaced with a Kunow sandstone floor (financed by voluntary contributions from community members). After 1876 the Polanowski Chapel was renovated. In 1898 a plan was drawn up for further enlargement of the church (it was still too small for the needs of the congregation), soon after, during the tenure of the next pastor, another plan was drawn up (he saw the project as very modest, the church should have aisles). Work began in 1908, still without a finished project. They were stopped by tsarist officials while the foundations were being laid. Another architect proposed building an entirely new church, but all plans were halted by World War I. In 1918 only a new sacristy was added to the church.
During the Second World War the church was damaged (the wall cracked) and the organ from 1884 was vandalized. A new organ was installed in 1969. Between 1975 and 1976 a new polychromy by Alojzy Goss from Toruń was made inside. In 2005 the relics of St. Florian were brought to Wilków. After the great flood of 2010, the church was extensively renovated.