A Church dedicated to St. Wilfrid has stood in York since medieval times. The original site of the Church was on land now occupied by the Judges Lodgings in Lendal and part of the Assembly Rooms behind in Blake Street.

In 1585 the parish could not support itself (possibly due to the large number of churches in York). The Church became redundant and was demolished. It was eventually built over and the parish united with St. Michael-Le-Belfry. St. Wilfrid's parish was revived by York Catholics in 1742 when they established their Misson in Little Blake Street. The Mission was founded by the Vicar Apostolic of the Northern District of England, Edward Dicconson.

A Catholic priest's house was established at number 7 Little Blake Street (now Duncombe Place) known as Chapel House. In 1760 the first public place of worship for Catholics opened in York. The chapel continued until 1802 when another chapel was built on the opposite side of the street (on the present site). At this time there were still strong anti-catholic feelings, so the chapel was hidden from the street by its presbytery. The chapel could hold 700 people and the Catholic population continued to increase in York.

In 1848 plans were drawn up to build a new Church. The funds, however, were diverted to build a much needed Church in the Walmgate area for the large number of Irish Catholics who settled there during the potato famine. St. George's Church was built and it became the Pro-Cathedral of the Catholic diocese of Beverley.

In 1859 York Corporation were planning a new approach road to Lendal Bridge. This prompted Dean Duncombe to apply to the corporation to continue the route by the chapel and towards the Minster. The old narrow lane (Lop Lane or Little Blake Street) was replaced with a wide thoroughfare. The houses on the opposite side to the chapel were demolished and the road widened to create Duncombe Place, named after the Dean.

St. Wilfrid's Church, as it stands today, was to be built on the site of the old chapel. The foundation stone was laid in April 1862 by Bishop Cornthwaite. The architect who designed the building was called George Goldie, son of a prominent parishioner Dr. Goldie. George Goldie was baptised in St. Wilfrid's chapel. He also designed St Wilfrid's Primary School nearby, however, he died in 1887 before the school was built.

The Church was designed in a Gothic Revival manner, a copy of 13th-14th century style. The arch over the main door has the most detailed Victorian carving in the city.

The Church was completed in 1864, costing around £10,000, and was opened by Cardinal Wiseman in June of that year. It was considered to be one of the most perfectly finished Catholic Churches in England, rich in sculpture and paintings and stained glass. It became the Pro-Cathedral Church of the Beverley Diocese. This was short lived as Beverley diocese was split to make the Dioceses of Leeds (South of the River Ouse) and Dioceses of Middlesbrough (North of the River Ouse). Nevertheless, St. Wilfrid's still stands as the "Mother Church of the city of York".

Part of the porch way believed to belong to the original St. Wilfrid's Church was found under the floor of the Assembly Rooms during the 19th Century renovations.

In 1945 Middlesbrough Diocese bought a 16th Century house in the Shambles. Number 35 is now the shrine of St. Margaret Clitherow. It is a pilgrimage site for Catholics from all over the world. Mass is celebrated here regularly every Saturday at 10.00am and it is open to visitors during the week.

St. Wilfrid's bell tower is 147 feet high. Ten bells were added to the tower in 1995.

In 2001 the Church was renovated.