Orii's shrew was first described, as a subspecies of the Dsinezumi shrew (Crocidura dsinezumi orii), by Kuroda Nagamichi in 1924; he named it after his collector, Orii Hyōjirō, who had provided the skin and skull of a single male from Amami Ōshima.

[2]: 3  This type specimen, damaged during the initial trapping,[2]: 3  was destroyed by fire in 1945.

[4]: 22  In their 1951 checklist, Ellerman and Morrison-Scott listed the shrew instead as a subspecies of the Greater white-toothed shrew (Crocidura russula orii).

[3]: 81  In 1961, after the recovery of a second individual from the stomach of a hime habu or Ryukyu Island pit viper (Ovophis okinavensis), Imaizumi Yoshinori elevated the shrew to species rank, based on morphological comparison with other species of Crocidura.

[4] In 1998, after the study of five further specimens from Amami Ōshima and Tokunoshima, Motokawa Masaharu [ja] confirmed this taxonomic treatment.