Sullivan applied chemistry to the development of Irish industry. After studying with Justus von Liebig at Giessen, he worked with Robert Kane at Dublin's Museum of Economic Geology, later the Museum of Irish Industry, becoming its chemist in 1846. His investigations ranged across minerals, agricultural materials, peat, and manufacturing processes. An 1845 paper described a test for phosphates in rocks, and he published widely on chemical and geological subjects.

He became professor of chemistry at the Catholic University of Ireland in 1856 and was elected to the Royal Irish Academy in 1857. He later taught theoretical chemistry at the Royal College of Science. His interests extended to Irish history and language: he edited Eugene O'Curry's work on the manners and customs of ancient Ireland and collaborated on historical publications. He advocated developing Ireland's resources through scientific training.

In 1873 he succeeded Kane as president of Queen's College Cork. He sought increased funding, expanded the grounds, and supported improvements to laboratories, the library, botanical collections, and student accommodation. His association with William H. Crawford helped secure the college observatory. The first women entered the college during his presidency in the 1880s. He also helped revive Cork's Literary and Scientific Society, promoted the Munster Dairy School, and participated in the Cork Exhibition of 1883. He remained president until his death in May 1890.