Following his studies at the Lycée Condorcet, he entered the École Nationale des Chartes where he wrote a thesis on the Cathedral of Senlis in 1907 and won the goodwill of his professor Robert de Lasteyrie.

In 1920, Aubert moved into the world of museums, taking a position at the Louvre as assistant to Paul Vitry in the department of Medieval, Renaissance, and Modern Sculpture.

He succeeded to Eugène Lefèvre-Pontalis' chair of Medieval Archaeology at the École des Chartes in 1924, where he taught for nearly 30 years.

He also taught at the École du Louvre as associate professor of Industrial Arts from 1921 to 1924 and as professor of Sculpture from 1940 to 1949, and at the École nationale supérieure des Beaux-Arts in the chair of French Architecture from 1929 to 1934 and the chair of Medieval Archaeology starting in 1937.

For more information, see Bibliographie des travaux scientifiques de M. Marcel Aubert, Paris: Société française d'archéologie, 1948, which contains all his publications up till 1948, 297 in number.