The Pillow Book by Sei Shonagon (c. 1000 AD, various translations) — Written by a court lady in Heian Kyoto, this is the most intimate portrait of the Kansai aristocracy at its height: gossipy, witty, obsessed with aesthetic refinement. Reading it before visiting Kyoto makes the temple aesthetic feel less alien.
Silence by Shusaku Endo (1966) — A Portuguese Jesuit missionary in 17th-century Japan confronts the persecution of Christians and his own faith. Set partly in Nagasaki but deeply embedded in the cultural logic of the period, this is one of the great Japanese novels and essential reading for understanding how Western religion encountered Japanese religious culture.
An Artist of the Floating World by Kazuo Ishiguro (1986) — Set in an unnamed Japanese city resembling Osaka or Nagasaki, Ishiguro's novel follows a painter reckoning with his role in wartime propaganda. The novel's portrait of postwar Japan and the difficulty of accounting for the past illuminates something important about the region.
Osaka Blues by Barry Lancet (2014) — A thriller set in contemporary Osaka, not literature exactly, but a readable way into the city's geography, social dynamics, and underworld before arriving.