In 1896 he enrolled in University College Dublin, graduating with a BA in 1900 and an MA in 1902. It was during his University years that Francis would become firm friends with James Joyce (1882-1941). It was Joyce who introcued Francis to the woman he would marry, Hanna Sheehy. He was a noted eccentric with an unusual style of dressing and a confirmed atheist. Francis was a vocal presence in the fight for women's suffrage and was often to be seen sporting a 'Votes for Women' badge. He was, at one stage, employed as a teacher by St Kieran's College in Kilkenny but resigned in protest against the College's refusal to admit women on the same terms as men. On the 3rd of June 1903 Francis and Hanna were wed. Rather than wear a suit and dress for their wedding, they were married in their graduation gowns instead. The two joined their surnames and styled themselves as the Sheehy Skeffingtons.
In 1912, Francis and his wife founded a paper called The Irish Citizen. The publication was pro-suffrage, pacifist, and nationalist in nature. They also founded the Irish Women's Franchise League, and organisation dedicated specifically to the cause of women's suffrage.
Never one to remain silent when faced with injustice, Francis spoke out against the conscription of Irish men into the British Army. His critiques culminated in a lecture given in 1905 which saw him arrested and sentenced to hard labour. He was denied that status of a political prisoner and as a result went on a hunger strike which saw him being released a week later.
Francis was involved in a number of political parties and issues throughout his life. He was a mediator during the Dublin Lock Out and became vice Chairman of the Irish Citizen Army.
During the 1916 Rising Francis was attempting to organise a civil defence group to prevent looting, but was himself arrested by the East Surrey Regiment as a sympathiser. On the 26th of April 1916, he was taken out by the Regiment with his hands bound as a hostage in a raiding party. During the course of the raids, Francis was shot and killed. Though attempts were made to cover up the murder, the truth came to light and his killer, Captain J.C. Bowen-Colthurst, was interred in an asylum after being determined of unsound mind.
At the time of his murder, Francis was quickly buried in the Barracks yard in Rathmines, but was later reinterred in Glasnevin Cemetery where he lies now.