In 1986, the United States Postal Service issued a 4¢ Great Americans series postage stamp honoring him.
Flanagan is a member of the Nebraska Hall of Fame.

On 25 February 2012, the Catholic Archdiocese of Omaha, Nebraska opened the canonization process of Flanagan.
At a 17 March 2012 prayer service at Boys Town's Immaculate Conception Church, he was given the title, "Servant of God", the first of three titles bestowed before canonization as a Catholic saint.
The investigation was completed in June 2015, and the results forwarded to the Vatican.
If the Vatican approves the local findings, Flanagan would be declared venerable.
The next steps would be beatification and canonization.

There is a portrait statue dedicated to Fr.
Edward J. Flanagan in Ballymoe in County Galway.
In 1986, the United States Postal Service issued a 4¢ Great Americans series postage stamp honoring him. Flanagan is a member of the Nebraska Hall of Fame.
On 25 February 2012, the Catholic Archdiocese of Omaha, Nebraska opened the canonization process of Flanagan. At a 17 March 2012 prayer service at Boys Town's Immaculate Conception Church, he was given the title, "Servant of God", the first of three titles bestowed before canonization as a Catholic saint. The investigation was completed in June 2015, and the results forwarded to the Vatican. If the Vatican approves the local findings, Flanagan would be declared venerable. The next steps would be beatification and canonization.
There is a portrait statue dedicated to Fr. Edward J. Flanagan in Ballymoe in County Galway.
Edward J. Flanagan