Novelist Jirō Nitta is his nephew and mathematician Masahiko Fujiwara is his grandnephew.

Born in the city of Suwa, Nagano Prefecture, Fujiwhara received his primary education at Takashima Common Elementary School and Suwa Higher Elementary School, where he was in the same class as future army general, Tetsuzan Nagata.

He joined the Central Meteorological Observatory (current Japan Meteorological Agency) in 1909 after completing undergraduate studies in theoretical physics at Tokyo Imperial University (now the University of Tokyo).

He started his tenure as a professor at Tokyo Imperial University in 1924, and succeeded Takematsu Okada as the fifth director of the Japan Meteorological Agency in 1941.

He retreated to the countryside afterwards to concentrate on his writing, and devoted his efforts to educating the future generation of meteorologists and researching meteorological phenomena such as vortices, clouds and atmospheric optics.