Although the concept of the Cathedral Church of St. John the Divine was first formulated around 1828, it only obtained official recognition when Rt. Rev. Horatio Potter, Bishop of New York, proposed the idea at the Diocesan Convention of 1872. The proposal received unanimous support. The New York state legislature granted a charter for the Cathedral in 1873 and fourteen years later, Bishop Potter and the Cathedral Trustees approved the purchase of the land on which the Leake and Watts Orphan Asylum had formerly been situated. With the charter granted and the location of the cathedral decided, Potter began the search for an architectural design that would do justice to the objectives of the cathedral project. In 1888 the Trustees sponsored a contest for the design of the Cathedral. The chosen design was submitted by Messrs. Heins and LaFarge of New York. The design, which called for a church five hundred and twenty feet in length, emphasized features of both Romanesque and Byzantine architecture (Harris 5-7).

In December of 1892, the cornerstone of the Cathedral was laid. However, complications closely followed the initiation of the project. The builders experienced problems laying the foundation. After two years of digging, they failed to reach bedrock. With the help of a donation from J.P Morgan in the amount of $500,000, the builders were finally able to hit bedrock seventy two feet below the surface level. Nonetheless, complications continued to plague the project. The death of Mr. Heins shortly after the completion of the choir section of the cathedral presented the Trustees with the opportunity to reevaluate the feasibility of the original design. Further incompatibility with the architectural firm to which Heins and LaFarge had both belonged led the Trustees to seek a contract elsewhere (Harris 9, 18).

Complications created by World War I followed by the Great Depression inhibited the progress of the Cathedral. Although it was, by far, not completed, the Cathedral was opened in 1941 just one day before the bombing of Pearl Harbor. As a result of the United States' entrance into the second World War, construction on the Cathedral was delayed.

The Rev. James P. Morton, who became Dean of the Cathedral in 1972, encouraged a revival in the construction of the Cathedral. In 1979 building of the Cathedral resumed and continues at the present time (Harris 24-26).