Napoleon III was passionately interested in history and archeology, and ordered digs, most notably in Alesia, Gergovia, and Bibracte to complete his biography of Julius Caesar.

[7][8] In 1864, Jean-Baptiste Verchère de Reffye, who was particularly involved in the project, proposed to the Emperor the project of a "historical museum" in order to: "provide historians with precise documents on the life of our Fathers, to invite industrial figures to study ancient manufacturing secrets, to get artists to recognise how art has evolved over time.

On 11 April 1866, the committee published a report detailing the main axes of the project, the organisation of the space (by age rather than by type of object, as was the practice in the past) and an estimate of the budget.

Starting in 1936, and following the rise in political tensions, the museum established plans to save the artifacts, a list of the most important pieces, and preparations for evacuations.

Minister of Cultural Affairs André Malraux, who was passionate about archaeology, planned an ambitious renovation project started in 1961 under the direction of René Joffroy.

The architect, André Hermant [fr], wanted to "calm the strange decor" of the château by covering some of Millet's restoration and windows.

[11] Among the most famous objects of the museum's Paleolithic collections is the Venus of Brassempouy, one of the earliest known realistic representations of a human face, discovered in 1892 in one of the numerous excavations of Édouard Piette in the Pyrenees.

The six rooms of the Gallo-Roman department presents evidence of the religious context (gods, the world of the dead), the presence of the Roman army in Gaul, the different types of crafts and everyday life objects (related to food, costume, ornament, transportation, writing ...).

[15] The first Middle Age (from the 5th to the 6th century AD) began with the Merovingian dynasty, founded by Clovis I. Gaul became progressively more Frankish and Christian.

One material witness to this Christianisation held by the museum is the syncretistic 7th-century Grésin plaque, believed to depict an ithyphallic Christ.

From this period, numerous cloisonné jewels were found with garnets set in metallic partitions, as well as buckles of damascened belts with silver or brass threads inserted in iron engraved furrows.

It is in this spirit that the "comparative archeology of the five continents room" was conceived at the beginning of the twentieth century by Henri Hubert and Marcel Mauss who wanted to illustrate "the ethnographic history of Europe and humanity" from the origins of man up to the Middle Ages.

Hubert conceived the general plan of this room according to two innovative ideas for the period: This comparative approach was popular in the nineteenth and twentieth centuries, although some comparisons did not survive a severe criticism (for example, the comparison of Magdalenian shoes with the Eskimos), but the comparative method, which was rigorously conceived and subjected under certain conditions, is omnipresent in any archaeological approach.

It is also a necessity to situate the ancient cultural phenomena in their space, to leave the limits of French territory and a nationalist approach.

Then he can compare the development and technical mastery of Bronze and Iron metalworkers in the Caucasus and Europe (objects from Cyprus, Greece, Italy, Spain, Hungary, Germany, Denmark, Sweden, Azerbaijan, North Ossetia, etc.).

From one continent to another and sometimes at different times, the exhibits show a similar state of development (transition from hunter-gatherer to producer), use of the same technique (Exploitation of flint or obsidian) or, on the contrary, very different forms or settings (Asia-America comparison, made possible by objects from China, Vietnam, Japan, Malaysia, Peru, Greenland, North America, etc.).

The other major collections arrived through Ernest Chantre for the series of the Caucasus or Jacques and Henri de Morgan with the products of their excavations in Susa (modern day Iran) and in the pre-dynastic necropolis of Egypt[18] Since 2014, the room is once again home to collections of Pacific origin, with the presentation of ethnographic series from Papua New Guinea.