The current structure, the congregation's fourth church, was designed by the architects Ralph Adams Cram and Bertram Grosvenor Goodhue in the French High Gothic Revival style and completed in 1914.

[12][6] This structure, in a neighborhood at the time dominated by the mansions of Manhattan's upper class, featured a prominent 260-foot (79 m) high tower and a bas-relief reredos by Augustus Saint-Gaudens and murals by John LaFarge.

[15] The third building was also the site of many high society weddings and funerals, including that of Consuelo Vanderbilt to Charles Spencer-Churchill, 9th Duke of Marlborough, the first cousin of Winston Churchill.

[17][14] The design by Cram and Goodhue won an architectural competition to build the new Saint Thomas Church, winning over entries by George Browne Post and Robert W.

In the wake of the September 11 attacks in 2001, Saint Thomas Church reached out to the British expatriate community in recognition of its Anglican heritage.

On October 28, 2002, the rector of Saint Thomas Church, Andrew C. Mead, was made an honorary Officer of the Order of the British Empire (OBE) by Queen Elizabeth II.

The honor was conferred at a ceremony at the British Embassy in Washington, D.C.[20] In October 2023 Saint Thomas Church commemorated the bicentennial of its founding in 1823, with an exhibition, lectures and special services.

[26] Saint Thomas Church has plain ashlar limestone exterior surfaces in the French High Gothic style.

Decorative archivolts above these niches and windows contain depictions of Thomas the Apostle's life, the sacraments, and the gifts of the holy spirit.

[29] To the left (south) of the main entrance, there is a square tower at the southeast corner of the church, facing Fifth Avenue and 53rd Street.

[26][18] The parish house is five stories tall and contains an oriel window in its eastern bay, separating it from the rest of the church.

[31] The windows for the present structure were designed beginning in 1929 by English stained glass artist James Humphries Hogan, who also the main American sales agent for the firm.

[17] The narthex, just inside the main portal, was originally decorated with symbols of four classical elements, four seasons of the year, and four angels.

[32] The elaborate reredos, gifted by the family of Harris C. Fahnestock, was designed by Goodhue and Lawrie and executed by the Ardolino Brothers.

[17][30] It is 80 feet (24 m) high, covering the west wall of the chancel, and consists of more than 60 stone figures relating to the discovery of Thomas the Apostle.

[25] In 1925, eleven years after completion, the north wall of the church was found to be bulging dangerously and hidden steelwork added.

The construction of the New York City Subway's 53rd Street Line in the 1930s prompted additional steel under the altar and massive reredos as a precaution.

Wallace Sabine, founder of the field of architectural acoustics, was hired to reduce reverberation in order to make the sermon more intelligible.

Beginning with the rectorship of John Andrew in 1972, however, it has informally followed the Anglo-Catholic or high-church tradition within the Episcopal Church that developed out of the Oxford Movement.

For masses at the High Altar, the Church uses a variation on the three traditional sacred ministers ad orientem, however as with many other Anglo-Catholic parishes that do not look to Tridentine Rome for liturgical cues, many of the unique traditional roles of sacred ministers are currently in use—the Deacon reads the Gospel and the Subdeacon reads the Epistle.

Since 2021, the 9 am Sunday Mass has become a Low-Church type children and family focused service, using Rite II and ad populum altar placed in the Chancel.

A robed children's outreach choir called the Noble Singers and composed of local girls and boys sings at the 9 am service.

The choir's primary function is to provide music for five services each week, as well as an annual concert series sponsored by the church.

In addition, the choir has toured throughout North America and Europe, performing at venues such as the Lincoln Center, Westminster Abbey, and the Vatican.

They have sung alongside artists such as Jessye Norman and Plácido Domingo, and gave the world-premiere performance of Andrew Lloyd Webber's Requiem, which was televised internationally by the BBC.

[10][38] The Loening-Hancock Gallery Organ was built as "Opus 27" of Taylor & Boody Organbuilders of Staunton, Virginia, in 1996 to honor Gerre Hancock for 25 years of service to Saint Thomas Church.

On October 3, 2008, Saint Thomas Church announced its Vestry's decision to replace the aging Arents Memorial Chancel Organ with a new instrument.

In addition to supporting the parish's internationally renowned liturgical and musical life, the Miller-Scott Organ serves as a showcase for recitalists from all over the world and helps Saint Thomas train the next generation of organists.

Much of the design and decoration form for the new organ case are derived from precedents throughout the rest of the building, and Gothic revival style in general.

Major carvings depict symbols of the Four Evangelists, and there are portraits of persons important in the recent life of Saint Thomas Church, including former directors of music Gerre Hancock and John Scott, Rector Emeritus Fr.