In 1891, Joel Asaph Allen was the first to scientifically describe Transandinomys talamancae, when he named Oryzomys talamancae from a specimen from Talamanca, Costa Rica. He placed it in the genus Oryzomys, then more broadly defined than it is now, and compared it to both the marsh rice rat (O. palustris) and to O. laticeps. Several other names that are now recognized as synonyms of Transandinomys talamancae were introduced in the following years. In 1899, Allen described Oryzomys mollipilosus, O. magdalenae, and O. villosus from Magdalena Department, Colombia. Oldfield Thomas added O. sylvaticus from Santa Rosa, Ecuador in 1900 and O. panamensis from Panama City, Panama, in 1901. In the same year, Wirt Robinson and Markus Lyon named Oryzomys medius from near La Guaira, Venezuela. Allen added O. carrikeri from Talamanca, Costa Rica, in 1908.
Edward Alphonso Goldman revised North American Oryzomys in 1918. He placed both panamensis and carrikeri as synonyms of Oryzomys talamancae and mentioned O. mollipilosus and O. medius as closely related species. O. talamancae was the only member of its own species group, which Goldman regarded as closest to Oryzomys bombycinus (=Transandinomys bolivaris). In 1960, Philip Hershkovitz listed talamancae, medius, magdalenae, sylvaticus, and mollipilosus among the many synonyms of "Oryzomys laticeps", a name later replaced by "Oryzomys capito". The species remained lumped under Oryzomys capito until 1983, when Alfred Gardner again listed it as a valid species, an action more fully documented by Guy Musser and Marina Williams in 1985. Musser and Williams also found that the holotype of Oryzomys villosus, the affinities of which had been disputed, in fact consisted of a skin of O. talamancae and a skull of the Oryzomys albigularis group (equivalent to the current genus Nephelomys). They restricted the name to the skin, making villosus a synonym of O. talamancae. They also examined the holotypes of panamensis, carrikeri, mollipilosus, medius, and magdalenae and identified them as examples of Oryzomys talamancae. Additionally, they included sylvaticus and Oryzomys castaneus J.A. Allen, 1901, from Ecuador as synonyms, but without examining the holotypes. Musser and colleagues reviewed the group again in 1998 and confirmed that sylvaticus represents Oryzomys talamancae; however, they found that castaneus was in fact an example of Oryzomys bolivaris (the current Transandinomys bolivaris).
In 2006, Marcelo Weksler published a phylogenetic analysis of Oryzomyini ("rice rats"), the tribe to which Oryzomys is allocated, using morphological data and DNA sequences from the IRBP gene. His results showed species of Oryzomys dispersed across Oryzomyini and suggested that most species in the genus should be allocated to new genera. Oryzomys talamancae was also included; it appeared within "clade B", together with other species formerly associated with Oryzomys capito. Some analyses placed it closest to species now placed in Euryoryzomys or Nephelomys, but with low support. Later in the same year, he, together with Alexandre Percequillo and Robert Voss, named ten new genera for species previously placed in Oryzomys, including Transandinomys, which has Oryzomys talamancae (now Transandinomys talamancae) as its type species. They also included Oryzomys bolivaris, which was not included in Weksler's phylogenetic study, in this new genus. The two species are morphologically similar, but Weksler and colleagues could identify only one synapomorphy (shared-derived trait) for them: very long
superciliary vibrissae (vibrissae, or whiskers, above the eyes). Transandinomys is one of about 30 genera in Oryzomyini, a diverse assemblage of American rodents of over a hundred species, and on higher taxonomic levels in the subfamily Sigmodontinae of family Cricetidae, along with hundreds of other species of mainly small rodents.
Several common names have been proposed for Transandinomys talamancae, including "Talamanca Rice Rat", "Transandean Oryzomys", and "Talamancan Rice Rat".