As Aboite Township began to grow in the 1980s, so did the Catholic population southwest of Fort Wayne. Priests from nearby St. Joseph Catholic Church began saying Mass for families in the area at Haverhill Elementary School until on January 1, 1988, Bishop John M. D’Arcy announced the establishment of a new parish to be called St. Elizabeth Ann Seton, pastored by Father Robert Schulte. By 1989, ground was broken on the corner of Aboite and Homestead Roads, and the church was completed the following year. Included in the construction was a smaller daily Mass chapel and a small adoration chapel. Renovations to repair and beautify the church began under the fourth pastor, Father Terry Coonan in 2023, removing the adoration chapel, but improving lighting, sound and visual impact of the church itself.

The Aboite area continued to grow (annexed into the city in 1996), and with it the parish that would become the second-largest Catholic church in Fort Wayne, growing from 375 families to over 2,000 registered families. It has become something of a training ground for new young priests, often assigned to the parish as parochial vicars before receiving their first pastorship. Thus far, four sons of the parish have been ordained to the priesthood and one daughter has become a cloistered Dominican sister.