John Thomas Aloysius Flannagan (1860–1926) was 19th and 20th century Catholic priest who served as the second president of St. Ambrose College in Davenport, Iowa from 1891 to 1906.
Flannagan was born in Haverhill, Massachusetts, and was ordained a priest for the Diocese of Davenport by Bishop Henry Cosgrove in Iowa City in 1885.
While he was president of St. Ambrose his own sister, Sr. Mary Editha Flannagan, BVM, ran Immaculate Conception Academy for girls, also in Davenport.
A baseball field was constructed on campus, and football was played even though it was not considered gentlemanly.
[4] Flannagan went to Sacred Heart Cathedral parish as rector after his term as president in 1906.