Holtz classified Bagaraatan as a basal tyrannosauroid, Coria identified it as a troodontid, and Rauhut placed it in Maniraptora.
Holtz, Coria, and Rauhut all provided distinct taxonomic placements for Bagaraatan, with Holtz placing it in the tyrannosauroid lineage, Coria identifying it as a troodontid, and Rauhut assigning it to the Maniraptora group.