It is located in the Roman Catholic Diocese of Lincoln and is the consolidated school of nine Catholic parishes in Nebraska City, Paul, Julian, Syracuse, Peru, Auburn, Avoca, and Plattsmouth.

Falling enrollment led to the closure of Saint Mary's in 1891, with the building being sold to the Nebraska City Public Library Committee, and in 1908 Annunciation Academy closed because of insufficient funds to repair the building.

The following year Saint Bernard's Academy was opened in the former home of a local judge, William Hayward.

[3] It was coeducational, with boarding facilities for girls, and was operated by the Bernadine Madames of Ollignies, Belgium, until 1920, when the Ursuline Sisters of Kentucky replaced them after passage of a state law disqualifying non-citizens from teaching in schools.

In 1927, the Ursulines took over Saint Benedict's also, and that school moved into a new building in 1951.