He was born near Omagh, County Tyrone and educated at University College Dublin. After graduation in 1909 he carried out research in the Physics Department under Professor John A. McClelland on the electrical charge of rain. He was awarded D.Sc in 1917.
In 1920, he succeeded McClelland as Professor of Experimental Physics, guiding research into atmospheric electricity and aerosols. Together with his brother, Patrick J. Nolan, and their students, they studied ionization, equilibrium and the relationships of small and large ions in the lower atmosphere. He also, with V. H. Guerrini, developed in 1935 the diffusion battery for measuring the size of aerosol particles.
When the School of Cosmic Physics was established at the Dublin Institute for Advanced Studies in 1947, John J. Nolan was appointed as its inaugural Chairman. He served until his death in 1952, and was succeeded in this position by Ernest Walton.
In 1920, he was elected a Member of the Royal Irish Academy, becoming Secretary in 1923 and President from 1949 to 1952. He was also Registrar of University College Dublin from 1940 until his death. In 1952, he died while lecturing a large class at UCD in Earlsfort Terrace. He was succeeded as professor of physics at UCD in 1953 by his former student T. E. Nevin, whose M.Sc. thesis under Nolan was on "The Effect of Water Vapour on the Diffusion Coefficients and Mobilities of Ions in the Air,"