Upton over the years has had three Parish Churches, each one in a different location and each with its own burial ground. The first parish church was the Norman Church, which stood by Moreton Road. The second was the Greenbank Church, which stood on Greasby Road and the third is St Mary's, the current parish church which stands on Ford Road. It is possible that there was a Saxon Church on the same site as the Norman Church.

In 1689 the Act of Toleration allowed non-conformists to have their own places of worship. A chapel was opened in Upton and Thomas Lea became the minister in 1690. The last minister seems to have been Thomas Woodcock, the chapel closing following his death in 1728.

There are currently only two churches in Upton:

• St Mary's Church, the Church of England Parish Church in Ford Road
• St Joseph's Church, the Roman Catholic Parish Church in Moreton Road

Until recently, there were two other churches:

• The United Reformed Church in Ford Road which closed in July 2015.
• The Jubilee Church, which met in Overchurch School, has moved to its own building in Wallasey