Among non-avian dinosaurs, troodontids are relatively rare but diverse. The Nemegt Basin in the Mongolian Gobi Desert, which incorporates three of the most fossiliferous beds in the world, is one such region with high troodontid diversity and has also produced eight troodontid taxa until now. The diversity of troodontids is biased towards the two formations, Nemegt and Djadochta. Despite its rich vertebrate fossil record, no troodontids have been described from the Baruungoyot Formation. This faunal absence is perplexing as the Baruungoyot Formation has often been considered intermediate between the other two units in stratigraphy and paleoenvironment, but there are no definite troodontid materials that could fill this ‘gap.’ Here, we report a new troodontid, Harenadraco prima gen. et sp. nov., from the Baruungoyot Formation in Hermiin Tsav, Mongolia. It is represented by an incomplete skeleton that mainly consists of partially articulated left hind limb elements. Harenadraco is small and lightly built like other troodontids, but its tarsometatarsus exhibits extreme slenderness comparable only to Philovenator among cursorial non-avian maniraptorans. It also implies high cursoriality that could be an adaptation of Harenadraco to its environment where potential prey animals like mammals and predators such as eudromaeosaurs were likely to be agile. The discovery of Harenadraco confirms the presence of troodontids in all three formations in the Nemegt Basin.