His father was André-Hippolyte Lemonnier, a poet, art collector and Secretary of the Académie de France à Rome.
His grandfather, Anicet Charles Gabriel Lemonnier, was a painter of historical subjects.
He was a student at the Lycée Charlemagne, then entered the École Impériale des Chartes, where he became an archivist-paleographer in 1865, with a thesis on Roman administration under the Visigoths.
His first major project involved the creation of an art library, with a collection of prints, photographs, and sculptural casts.
Shortly after his retirement from the Sorbonne in 1913, he was elected to the Académie des Beaux-Arts, where he took Seat #2 in the "Unattached" section, succeeding Jules Comte, who had died the previous year.