O'Mahony resigned from his post with the National Board of Education, and the National schools of Ireland, in 1863 to concentrate on his work with the IRB and its newspaper The Irish People. He remained on the paper's staff as assistant bookkeeper and part-time journalist until it was raided and closed down in 1865 when the British felt that an armed uprising was imminent. At that time he was arrested along with Charles Kickham, Thomas Clarke Luby, John O'Leary, Jeremiah O'Donovan and others. The charges laid at Kilmainham Gaol included, "Conspiring To Depose The Queen, To Compel Her Majesty To Change Her Measures And Counsels, To Move And Stir Foreigners To Invade Ireland" An abortive uprising known as the Fenian Rising took place in 1867 but was quickly put down.