The cornerstone was laid on August 22, 1893, barely fifteen months after the parish was organized. The following winter appears to have been a mild one, because St. Thomas’ was ready to house its first service on February 25, 1894.

The church building is a combination of Queen Anne and Stick styles of architecture, with some Gothic touches. The former St. Stephen’s Church in Romulus, NY, appears to have been built from the same plans, although it has less ornamental detail. The architect for both was probably a Mr. Haight, of Ovid, NY.
Virtually all of the furnishings are original. In the early 1970s the altar area furniture was shifted to increase space, and pews in the front portion of the nave turned 90º to provide a more intimate setting for worship. St. Thomas’ remains the least-altered Victorian village church in the area.
The stained glass windows are original, and have been restored by the Jerome Durr Studio.  In 2012, Mr. Durr created the stained glass pane above the Narthex entrance which honors long time rector, Father Cullie Mowers.
In 1991, preparing for the congregation’s Centennial, all of the movable furnishings were stored and services relocated to the nearby Ellis Hollow Community Church for three months while the interior was extensively repaired and repainted in its 1893 colors. The floors and woodwork were cleaned and resealed by hand to preserve their original appearance, and new seat cushions and carpet runners were provided. The building was listed on the New York State and National Registers of Historic Places in 1993 and 1994, respectively. In 1998 the exterior was renovated and repainted in a color scheme derived from traces of the original paint discovered during carpentry repairs; the parish received a citation for this work from Historic Ithaca & Tompkins County.
The ceramic Stations of the Cross, by Dirk Slabbinck of Belgium, were installed in 2005.