Kyoto Journal was founded in 1986 by editor and designer John Einarsen, whose editorial vision was heavily influenced by publications like CoEvolution Quarterly, which blended arts, spirituality, and Asian cultures. The magazine grew out of the expatriate scene of Kyoto in the 1980s, namely a monthly series of literary get-togethers at Einarsen's home, which eventually grew into the local institution of open-mic nights and poetry readings known as The Kyoto Connection, organized by editor Ken Rodgers.
The magazine was awarded the Utne Reader's prestigious Independent Press Award for Excellence in Art & Design in 1998, and it has been regularly shortlisted for General Excellence, Local/Regional Coverage, Writing Excellence, and Best Essays.
Until 2011, it was published by Harada Shokei of Heian Bunka Center, a Japanese calligraphy school in Kyoto. After the publication of 75 full print issues, the magazine announced in December 2010 that it would switch to digital editions beginning with issue 76.