While he played at underage level for Tipperary, John Flanagan made his first appearance for the Tipperary Senior Hurling team during the 1967 championship and was a regular member of the starting fifteen until his retirement a decade later.
John Flanagan worked at Erin Foods, Thurles for many years and up to the time of his death.
Along with his father he was involved at committee level in the nationally recognised Holycross Horse Show which ran for many decades into the 1990's.
John Flanagan passed away suddenly on the 9th of September 1994 at his home in Galbertstown, Thurles, Co. Tipperary.
He is buried in the graveyard adjacent to Holycross Abbey, Thurles, Co. Tipperary.