Egan was born in Ballymahon, Co. Longford, Ireland. His family later moved to Dublin and at the age of fourteen he entered the office of an extensive grain and milling firm, the North City Milling Company, in Dublin, and before he was twenty had been promoted to the post of chief bookkeeper and confidential man. Later he was elected managing director of this, as a stock company, it being the most extensive one in Ireland. He was, at the same time, senior partner in the most extensive bakery establishment in the county. He had been an industrious learner before going into business, and all this time took evening lessons of various instructors, and particularly of a brilliant young Episcopal minister of Dublin named Porte."
Egan became involved with the Irish Republican Brotherhood soon after its establishment. He and others (including John O'Connor Power, Joseph Biggar and John Barry) resigned from the Irish Republican Brotherhood in August 1877 over the condemnation by its leaders of the use of politics within a revolutionary organisation.
In 1873, Egan was treasurer of the Irish Republican Brotherhood, and with the IRB's supported, participated in the establishment of the Home Rule League with fellow IRB Supreme Council members John O'Connor Power, Joseph Biggar and John Barry.
At its foundation in 1879, he was elected treasurer of the Irish Land League. He was a close associate of Michael Davitt and Charles Stewart Parnell. At the end of 1880, he, with twelve others, including Parnell, Dillon, Bigger, Sexton, Sullivan, Sheridan, and Matt Harris, were singled out by the government for prosecution for alleged conspiracy. After a costly trial of sixteen days the jury stood ten for acquittal and two for conviction. The government did not dare arraign them again, but brought in a bill to suspend the habeas corpus act, and to permit the arrest of any one obnoxious to the government, intending to proscribe all members of the league.
Following the arrest of Parnell, in his function as Treasurer of the Land League he signed the No Rent Manifesto of 18 October 1881. This led to proscription of the League by the British government. This led Egan to flee to Paris with the organisation's funds in order to prevent their confiscation by the authorities. He remained in Paris from February 1881 to the end of 1882.
Between 1880 and 1882, Egan was nominated a number of times for election to parliament, and was twice unanimously nominated, once for Queen's County and again for Meath, but he declined because he could not take the oath of allegiance to England required by the government.
Learning that the government was conspiring to arrest him and colleagues, and make him the victim of a pretended trial, he quietly fled to the Netherlands, and later fled to the United States, settling in Lincoln, Nebraska, where he continued to work strenuously for the Irish Land League and Irish home rule. In 1881 he was elected, at its convention in Boston, president of the National Executive Committee of the Irish National League of America.
Nothing new has developed yet to talk about. What has been said so far is simply a rehash of charges, without proof, that has been made for the last five years. But wait until the evidence for Parnell is produced. The whole Times' case will be exploded and indisputable evidence produced which will show Parnell guiltless and the true character of the allegations against him. You may expect some sensational testimony ... I have no doubt of the complete vindication of Parnell and all his associates and this will greatly injure the government.
As United States Minister to Chile (1889-93), he represented the United States when relations were strained during the revolt against President José Manuel Balmaceda. He caused the Baltimore Crisis. The general Chilean attitude was probably best expressed by Eduardo Phillips, Chief of the Diplomatic Section of the Ministry of Foreign Relations, who described Egan in a letter to one of the newspapers as a person "utterly lacking in all elements of culture and courtesy, and ever-ready to descend to the level of invective and calumny". He sought to provoke the United States into a war of colonization against Chile.
Ninety-eight per cent of all Irishmen were not in sympathy with the revolt, and England had nothing to gain by shooting people after it is over ... If anyone were shot it should have been John Devoy who hatched the whole nefarious scheme here in New York and was personally responsible for it.
Egan was the father of fourteen children, nine of whom survived childhood. His residence in Lincoln was located at 1447 Q street.
"In gay Paree he hides, Egan of Paris, unsought by any save me. Making his day's stations, the dingy printing case, his three taverns, the Montmartre lair, rue de la Goutte d'Or, damascened with flyblown faces of the gone." From James Joyce's, Ulysses.