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One of the highest mountains located in Japan. It is featured in many pieces of Art ,and media.
Anime / Manga
Being one of the most renowned natural landmarks in all of Japan. It comes as no surprise that this sacred mountain has made appearances in many manga and anime series. Sometimes as part of the scenery of the island nation, and sometimes as part of the plot.
Code Geass
In the anime/manga series Code Geass. Mount Fuji was a rich source of a rare mineral called sakuradite. This mineral was a source of power for the Knightmare Frames(KMFs) that were used by the Britannian Army. Japan was invaded, and the sacred mountain was desecrated as it was mined for this resource.
Near the end of the second season of Code Geass, Code Geass R2. Lelouch blew up much of Mount Fuji using the volatile mineral to amplify a bomb he had planted as part of his strategy. This massive reaction obliterated much of the Black Knights' resistance to his own army.
Nagasarete Airantou

Airan Island's Mt. Fuji
In the manga/anmie series Nagasarete Airantou. The snow capped mountain on the island of Airan Island is also named Mount Fuji. Many of the original inhabitants were of Japanese decent. Stranded on this isolated island with no hope of rescue. The people most likely named the mountain of the island after the original Mount Fuji to make the environment feel more like a part of their home.