In the past Tubbergen had a chapel dedicated to Sint Pancratius (Saint Pancras), which was served from Ootmarsum. This chapel was expanded and served as the parish church for the town from 1576 onwards. In 1634, a priest was appointed.

Although the population remained largely Roman Catholic, the church passed into Protestant hands. When Lodewijk Napoleon heard in 1809 that there were only 68 Protestants living in Tubbergen compared to 1.000 Catholics, he ordered the return of the church.

In 1896, construction began on the current Sint Pancratius Basiliek. A year later the dedication ceremony took place. The Gothic tower dates from the early 16th century and was erected using sandstyone from Bentheim. In 1978, the tower was raised in height by three metres.

On 6 January 2000 the church was elevated to the status of Basilica Minor by the Vatican.

Sint Pancratius Basiliek. is well known for its precious stained-glass windows, which were crafted by five generations of the Nicolas family of glaziers. The first windows were installed in 1897 upon completion of the new church. The last windows date from 2002.