Neocosmocercella bakeri n. sp. is described from the large intestine of Phyllomedusa vaillantii Boulenger collected in the Caxiuanã National Forest in the Eastern Brazilian Amazon. The new species is easily distinguished from the type-species of the genus, Neocosmocercella paraguayensis Baker & Vaucher, 1983 in possessing a triangular mouth opening with three simple lips (vs three bi-lobed lips and hexagonal mouth opening) and somatic papillae, which are absent in N. paraguayensis. The males of the new species are distinguished by the distribution of the sessile cloacal papillae and the dimensions of the gubernaculum, whereas the females are distinguished by their smaller size and opisthodelphic uterus. This study expands the diagnostic characters of Neocosmocercella Baker & Vaucher, 1983, reports the first species parasitising anurans of the Brazilian Amazon, a new host record for the genus, and the description of the second species of the genus.