While at University College Dublin (UCD), she founded the Department of History of European Painting in 1965, and was head until she retired in 1974.

She published La sculpture irlandaise pendant les douze premiers siècles de l'ère chrétienne in 1933, with a dedication to Focillon.

Her first major work, Irish art in the early Christian period, was published in 1940, and focused on an area of study largely untouched since Margaret Stokes in the 1800s.

The book charts Irish art from the prehistoric up to the twelfth century, covering sculpture, manuscripts, and metalwork.

Through UCD she worked alongside Eoin MacNeill, R. A. Stewart Macalister, Gerard Murphy, Seán P. Ó Ríordáin, and Rúaidhrí de Valera.

Amongst her close friends with whom she shared mutual research interests were Máirín Bean Uí Dhálaigh, Mairín Allen, and Frank O'Connor.

[3] During World War II, she was involved in the evacuation of objects from French and London museums, acting as the secretary of the commission for the preservation of works of art in occupied Europe.

[3] From 1946, Henry resumed her field work, recording monuments and some excavations at sites such as at the Inishkea Islands and Glendalough.

As a result of her work, the department of archaeology held a photographic archive documenting early Irish Christian art as well as comparative material.

[8] An exhibition of her original papers, notes, journals and sketches titled "Françoise Henry and the history of Irish art" was held in the RIA.