Nepenthes muluensis was first collected by Mitsuru Hotta on March 18, 1964, on Mardi between the third and fourth camps on the western ridge of Mount Mulu, Sarawak. The holotype, M.Hotta 14791d, is deposited at the Botany Department of Kyoto University (KYO). Hotta described the species in 1966, naming it after Mount Mulu, to which it was thought to be endemic. The description did not cover the lower pitchers of this species, which were unknown at the time. Nepenthes muluensis was the first Nepenthes species to be described in 26 years (after N. densiflora in 1940) and the first since the end of World War II. At this time the genus was experiencing a revival in global interest, thanks largely to the work of Shigeo Kurata.