At the age of twenty-one he entered the École Normale in Paris, and from 1853 to 1858 he held the appointment of keeper of the scientific collections. In 1877 he became professor of natural history in the chair of geology at the Collège de France, in Paris, succeeding Charles Sainte-Claire Deville. In 1881 Fouqué was elected a member of the Academy of Sciences.
As a stratigraphical geologist he rendered much assistance on the Geological Survey of France, but in the course of time he gave his special attention to the study of volcanic phenomena and earthquakes, to minerals and rocks; and he was the first to introduce modern petrographical methods into France. He also worked on volcanic gas analyses, using the methods of Robert Bunsen, mainly with his student Henri Gorceix on Santorini (Greece). One prominent student of his was Alfred Lacroix, to whom Fouqué's daughter was married.
His studies of the eruptive rocks of Corsica, Santorini and elsewhere; his researches on the artificial reproduction of eruptive rocks, and his treatise on the optical characters of feldspars deserve special mention; but he was perhaps best known for the joint work which he carried on with his friend Auguste Michel-Lévy.
His chief publications were: Santorin et ses éruptions, 1879; (with Michel-Lévy) Minéralogie micrographique, Roches éruptives françaises (2 vols., 1879); and Synthèse des minéraux et des roches (1885).