In 1975, Fr. Michael Spillane was assigned to Our Lady of the Fields in Millersville to establish a mission parish in Crofton.  Prior to Fr. Spillane's assignment, Crofton Catholics had registered with and attended Mass at Our Lady of the Fields.  Fr. Spillane celebrated the first Mass here in the Crofton Woods Elementary School auditorium with 1,000 people in attendance.  One of the events, which helped the Crofton Mission establish its identity quickly, was the canonization of the first American-born saint on the same weekend that Mass was first celebrated publicly in Crofton.  Fr. Spillane immediately asked for and received permission to dedicate the Mission to Elizabeth Ann Seton, and Archbishop Borders did that formally in November 1975.

By the end of 1976, Archbishop Borders made Seton Mission a parish with Fr. Spillane as its first pastor.  The parish then had close to 600 families.  After a careful search, 48 acres of land were located on Rt. 424, which the parish purchased from the Episcopal Cathedral Foundation of Washington in September 1977, and subdivided, retaining 19 acres for construction of the church.  The first Masses in the new facility were celebrated on July 18 and 19, 1981.

The stained glass windows that highlight the nave of St. Elizabeth Ann Seton Church were originally designed and executed by Franz Mayer of Munich, Germany in 1927.  Until 1978, the windows graced the chapel of the Jesuit seminary at Woodstock, Maryland.  When the Jesuits sold the building to the state of Maryland for use as a Job Corps Training Center, the Baltimore Archdiocese negotiated to obtain the stained glass windows.  Fr. Spillane requested that the windows be reserved for use in Seton's church.  A brochure titled Prayers in Glass:  Seton's Windows, written by James R. Schaefer, PhD, describes the windows and the biblical story each tells.  This brochure is available in the church vestibule bookracks.

The fourteen Stations of the Cross were obtained from the Generalate of the Sisters of Mercy in Potomac, Maryland, when the building was closed in 1980.  Designed by Ranieri Studios of Detroit, Michigan, the stations are modeled on original paintings found in St. Ann Church, Munich, West Germany.  The stations were made in Italy, c. 1959, each one carved from a solid block of Carraramarble.  The background of gold glass mosaic gives added emphasis to the figures in each station.

Cast by the McShane foundry of Baltimore in 1913, the four bronze bells over the main church entrance originally hung in St. John the Evangelist and St. James Church on Valley and Eager Streets, Baltimore.  Tuned to ring the Westminster chimes, the bells are named for Mary Ever Virgin, St. Bernard, St. George, and St. John the Evangelist.  Two of the bells are memorialized to former pastors of St. John's:  Msgr. Bernard MacManus (1853-1888) and Msgr. George Devine (1888-1913).