At the site of the apparition of Saint Anne to a local villager, Wojciech Głowa, a wooden cross was first erected, followed by a small wooden chapel. The site of the apparition quickly became famous for miracles and graces received through the intercession of Saint Anne.
Soon, news of the miracles reached the clerical authorities, who appointed a commission to investigate the events taking place at the cross. The Bishop of Kujawy, Paweł Wołudzki, having become convinced of the graces flowing to the villagers, decided to build a wooden church under the invocation of Saint Anne nearby, 300 steps to the north-west, where the current temple is located.
He sent one of the priests to this place to take care of the pilgrims. However, he was unable to cope with the growing number of pilgrims.
In 1639, Bishop Mateusz Łubiński entrusted this sanctuary to the Conventual Franciscans. They began to organize monastic life and serve the pilgrims.
In 1657, during the Swedish Deluge, the monastery and church suffered significant damage.
Work on the construction of a brick church began during the term of office of the guardian of Smardzewice, Fr. Hadrian Kozłowicz, in 1683. The construction was completed in 1699, it was a votive offering of the Bishop of Warmia, Stanisław Zbąski, to Saint Anne for graces received, especially for the gift of health. The church was consecrated on November 6, 1701, by Bishop Andrzej Albinowski, suffragan of Kujawy. The parish was canonically erected on July 26, 1775, by the Bishop of Włocławek, Antoni Kazimierz Ostrowski.
The founder of the brick monastery, next to the church, was the Bishop of Kujawy, Krzysztof Antoni of Stupowo Szembek, later the Primate of Poland. Thanks to him, the monastery was built in the years 1722-1746 and the existing church was surrounded by a wall.
Because of the Franciscans' support for the January Uprising, on November 21, 1864, the tsarist government dissolved the order in the Russian partition, including the Franciscan monastery in Smardzewice. The land of the Smardzewice monastery was parceled out, and the management of the parish was entrusted to diocesan priests. During World War I (1914-1918), the church was partially destroyed. After Poland regained independence in 1918, the church buildings and the monastery began to be restored.