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The parish "was founded in 1908 by the Rev. P. J. Mahoney, D.D.", the parish's first pastor, formed in response to "…the rapid growth of the city along the Hudson River above 145th Street…". Mass was said in a store until the erection in 1910 of a two-story building, which serves as a school and church. Ground for a church adjoins the school building on the corner of 175th and St. Nicholas Avenue". In 1914, the Rev. Dr. Mahoney was still pastor and was assisted by the Rev. Francis A. Kiniry and Rev. Joseph V. Stanford, the three of whom occupied a recently completed "handsome three-story rectory".
Soon after his arrival in the United States in 1951, Fr. Ivan Illich was made an assistant priest of the parish. He preached under the name of John Illich, at the suggestion of the Parish's pastor, who claimed that the name Ivan "sounded communist". At Incarnation, Illich rose to prominence as an ally of the large Puerto Rican community in Washington Heights, organizing cultural outlets for them, such as the San Juan Fiesta, a celebration of Puerto Rico and its patron saint which eventually evolved into the still-extant Puerto Rican Day Parade. The success of Illich attracted the attention of the Archbishop of New York, Cardinal Spellman, eventually resulting in Illich's naming as vice-rector of the Catholic University of Puerto Rico in 1956.
The current pastor is Reverend Edward Russell.
Building
The present Gothic Revival stone buttressed-church with apse was built in 1928 to the designs of W. H. Jones with two small towers.
Internally, the contemporary-with-the-building baldacchino is of white marble and lit by rich stained-glass windows. "At the West End is a large and stunning rose window above the gallery. Twin organ facades with gold pipes face into the gallery from both sides, and additional organ facades are found in the North transept and in the apse".