Is Napoleon in the Panthéon?

No. He is at Les Invalides, under the Dôme, and he has never been in the
Panthéon. The confusion comes from something real: it was Napoleon who, in 1806, returned
the Panthéon to Catholic worship while keeping its crypt for the burial of dignitaries of the Empire.
So he sent a great many people there — but not himself.
Napoleon liesAt Les Invalides, under the Dôme
Since15 December 1840
Tomb completed1861
The PanthéonCivilian great figures
Imperial dignitariesIn the Panthéon crypt
The 1806 decisionNapoleon returns it to worship
Two different logics
The Panthéon honours, by decision of the Republic, civilian figures: writers, scientists, résistants, statesmen and stateswomen. Les Invalides is a military complex where soldiers lie — marshals, generals — and, at the centre, a single sovereign. Napoleon fits into neither Panthéon category; he fits perfectly into the Invalides one, which he had himself helped to create by moving Turenne and Vauban's heart there.
The full comparison of the two monuments is on this page.
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Frequently asked questions
Is Napoleon buried in the Panthéon?
No, he has lain at Les Invalides under the Dôme since 1840.
Why the confusion?
Because Napoleon had many dignitaries of the Empire buried in the Panthéon crypt from 1806.