Currently, marsupials (modern members of the Metatheria clade) are widely distributed in tropical and subtropical areas of South America, but poorly represented in the fossil record of these regions. Except for the species-rich fossiliferous localities of La Venta in Colombia, additional Miocene metatherians from tropical, equatorial South America are sparsely reported in Bolivia, Brazil, Peru, and Venezuela. Here, we introduce new metatherian remains recovered from the late middle Miocene locality of TAR-31, San Martín Department, Peru, which has been assigned to the Laventan South American Land Mammal Age (~13 Ma) by mammalian biostratigraphy. Three metatherian taxa are recognized at TAR-31: the didelphid didelphimorph ‘Thylamys’ cf. ‘T.’ colombianus, and the paucituberculatans aff. Palaeothentes and Pitheculites ipururensis sp. nov. This assemblage and the presence of a cebid primate at TAR-31 suggests predominantly humid and warm tropical conditions, with the occurrence of both forests and drier habitats in the surroundings. Comparisons with other Miocene metatherian assemblages at low and mid latitudes of South America clearly confirm close relationships between TAR-31 and La Venta (agreeing with observations based on monkeys and rodents), as well as, to a lesser extent, with Acre River local faunas and Madre de Dios (MD-67) in Brazil and Peru, respectively. The current results support the hypothesis that Western Amazonia was a single and consistent biogeographical region for land mammals over middle Miocene times, at the western edge of the Pebas Mega-Wetland System, and highlight the role of the Amazonian region concerning marsupial Neogene radiation. U-Pb analysis made on detrital zircon grains from TAR-31 gave a maximum depositional age of 17.4 ± 0.12 Ma (i.e., 4 Ma older than the biostratigraphical age), with a mixed detrital source likely comprising Precambrian (Western Amazon Craton), Neoproterozoic (Neoproterozoic mobile belts), and Phanerozoic rocks (Andes).