From a samurai-class family of Ashigarashimo District, Kanagawa, Kitamura was interested in liberal politics at an early age, and played a minor role in the Freedom and People's Rights Movement.

He attended the Tōkyō Senmon Gakkō (which later became Waseda University), but was expelled due to his radical political views.

His attempts to explore the nature of the self and the potential for the individual, particularly in his seminal work Naibu seimei ron ("Theory of Inner Life"), are regarded by some[according to whom?]

Kitamura was also drawn to the Quaker movement, and founded a pacifist society, the Japan Peace Association (日本平和会), in 1889.

Kitamura authored the Bungakukai article The Evils of Blind Faith (頑執盲排の弊, Ganshūmōhai no hei), in which he ridiculed, among other things, the kokugaku movement, which by the time of its near-extinction in the late 19th century had evolved into a form of Shinto fundamentalism.