When Father J. M. Lancaster—a priest of considerable personal wealth—was appointed pastor, his primary objective was securing a permanent site for a new, larger house of worship.

At the same time, the First Presbyterian Church of Frankfort on Wapping Street was also expanding and seeking a new location. Rev. Eli Smith and his congregation offered their original property for sale.

On November 11, 1848, Father Lancaster purchased Frankfort's original Presbyterian Church building and lot on Wapping Street for the overcrowded St. Patrick's congregation. The purchase price was $5,000, with Father Lancaster paying $1,500 in cash and issuing a note for the remaining balance.

Father Lancaster contracted newly arrived brothers John Haley and Denis Haley to build the new brick structure. Throughout construction, the old Presbyterian building remained standing on the site so that celebration of Mass was never interrupted.

Upon completion of the new structure, the original Presbyterian meeting house was razed and the congregation moved into their new home, formally dedicated as the Church of the Good Shepherd. In 1860, Frankfort's first Catholic school was established.

Very few alterations have been made to the historic exterior over time:

• Choir Loft: Added after initial construction completed.
• Center Entrance Door: The original floor plan lacked a center entrance door, creating difficulty for funeral processions. Father Lambert Young contracted stonemason John Glenn to install a central entrance—despite local fears that cutting the opening might cause the steeple to crumble.
• Steeple Bell: Installed around 1869.