The church stands on the site of one dedicated to St Æbbe before 1005. Most sources suggest that this was the Northumbrian St Æbbe of Coldingham, but it has been suggested that Æbbe of Oxford was a different saint. The name was first recorded in about 1005 when the church was granted to Eynsham Abbey.

The present church was built in 1814–16. It was enlarged and improved in 1866 and 1904. A Norman doorway of the 12th century has been restored and placed at the west end, The church is the parish church for the parish of St Ebbes, a portion of which was demolished to make way for the nearby Westgate Shopping Centre in the 1970s. The church has a ministry among the remaining part of the parish, although most of its members live outside the parish. The church is a partner church of St Ebbe’s Primary School, a school within the parish.