Founded in 1641, St. Ignatius is one of the oldest Catholic Parishes in continuous service in the United States. Fr. Andrew White and other Jesuits sailed on the Ark and the Dove to help found an English Colony, permitting freedom of religion. Fr. White settled among the Potobac Indians at Chapel Point, learned to speak their language, and soon baptized their Indian Tayak or Chief.

Although often tried by repressive laws, the Jesuits continued to serve colonists, Indians, and slaves from the "olde wooden chapelle" by the point, and later from "Paradise Hill." Supplies from the Manor Farm were offered to the Americans attacking Yorktown. With the return of peace, the present church was built in 1798. It was blessed by John Carroll, the first bishop of Baltimore.

Though suppressed worldwide in 1773, the Society of Jesus was restored in America by those who took their vows in this church in 1805. From here, saddle priests rode forth to serve all of Charles County, as well as parts of Prince George's and Calvert Counties.

Union troops occupied St. Thomas Manor during the Civil War. Fire substantially destroyed the interior of the church and Manor House on December 27, 1866. However, by June 7, 1868, both were restored and rededicated.

For over 150 years, St. Thomas Manor at St. Ignatius was the home of Superiors of the Maryland Mission. Many missionaries lived and worked here. Courageous people worshiped here despite severe obstacles to their faith, and the famous visited for advice and counsel. From this manor, priests attended Catholics in an area from Virginia to Pennsylvania, developing new missions and establishing new residences. From here, all the older parishes of Charles County have been attended, and most were founded by priests of St. Thomas Manor.