In the early 1900s residents had to travel to St. Mary's Church in Hackensack for worship. It wasn't until 1912 that a group of people including Patrick Corcoran, George Herbert, Stephen Lazur and Bernard Morchen built the church on donated land along Washington Avenue.
The church was a mission parish of St. Mary's until 1940 when it successfully broke away and was named by the Archdiocese of Newark in honor of Margaret of Cortona, a 13th century Italian penitent canonized in 1728.
St. Margaret's has undergone various changes. A house was available for sale on property adjacent to the east side of the church, and it was purchased in January 1941 as the Rectory for St. Margaret’s from Frank and Amelia Hrbek. A parochial school for kindergarten to eighth grade was dedicated in 1957. The school was permanently closed after a 1986 arson fire.
By 1959, a second church was built on the other side of the same property with a new rectory, church and convent, and was completed in 1962. The old church was converted into a meeting hall and named after the founding Pastor, Rev. Robert F. Marnell.
October 29, 2012 - Superstorm Sandy ravaged Little Ferry with floodwaters rising to around 8 feet. St. Margaret's Church was among those damaged by the flood. The Church had to undergo major repairs and Masses were held in the Marnell Hall in the meantime.