Mr. Fuji looks after abandoned and orphaned Pokémon at the Lavender Volunteer Pokémon House in Lavender Town. He subscribes to Pokémon Fan Magazine. Mr. Fuji is supposedly shy. Mr. Fuji wishes for the happiness of all Pokémon. He cares for the Cubone that Team Rocket orphaned.
Mr. Fuji is not a native of Lavender Town. He used to live on Cinnabar Island, where he was known as Dr. Fuji, the founder of Pokémon Lab. He is a close friend of Blaine, as indicated by a portrait in the Cinnabar Gym in Pokémon FireRed and LeafGreen.
In the Generation I games and Pokémon FireRed and LeafGreen, when members of Team Rocket killed Marowak at Pokémon Tower, Mr. Fuji marched up to their hideout and started to rant about how Team Rocket was abusing Pokémon. Later, Mr. Fuji went to the Pokémon Tower to calm the Marowak's restless spirit, but Team Rocket appeared and held him hostage until the player drove them out of the tower. In gratitude, Mr. Fuji gives the player a 
Poké Flute.
In Pokémon Emerald, there is a message left at Faraway Island where a wild Mew can be found. The message pleads for only "a kindhearted person" to ever set foot on the island again.
In the Generation II games and Pokémon HeartGold and SoulSilver, Mr. Fuji does not have a prominent role. He is found in the House of Memories paying respects to the deceased Pokémon there. In the house, there are hidden chambers that only Mr. Fuji has access to.
It is rumored that Mr. Fuji once lived in the Pokémon Mansion, where journals related to the discovery of Mew and the birth of Mewtwo can be found. The mansion being located on Cinnabar Island and the fact that Fuji was a doctor are the only implications given.