The temple was established by Shimazu Takahisa in 1554 as a branch temple of the Shimazu family temple Fukushô-ji. The Ryukyuan scholar-official Chatan Chôshû died in Kagoshima in 1653 before departing for Edo, and was buried at Nanrin-ji.
It was dissolved in 1869 or 1870, along with a great many other temples in Satsuma domain, as part of the nationwide anti-Buddhist policy of haibutsu kishaku. Matsubara Shrine was established in its place, and remains on the site today.
Some twenty-three graves from Nanrin-ji were moved in 1922 to a new location in Kagoshima's Tokiwa-chô neighborhood, and are maintained today as a site known as the "Saigô Family Graveyard" (Saigô ke no haka).
- Ono Masako, Tomita Chinatsu, Kanna Keiko, Taguchi Megumi, "Shiryô shôkai Kishi Akimasa bunko Satsuyû kikô," Shiryôhenshûshitsu kiyô 31 (2006), 232.
- Signs on-site at Saigô-ke no haka, Kagoshima Tokiwa-chô 2-2-14.