Peramus is generally considered an advanced
cladotherian. In the analysis performed by Panciroli and colleagues (2018), Peramus was recovered as within a clade also including Palaeoxonodon and Amphitherium, as derived members of
Cladotheria. Peramus, Palaeoxonodon and Amphitherium were united by the shared traits of "convergence of the Meckel’s sulcus with the ventral border of the mandible; and possessing open rooted
postcanines." but the placement of Peramus as a more advanced cladotherian cannot be ruled out.[4] In a 2018 analysis by Bi and colleagues, Peramus was recovered in a clade with Palaeoxonodon and Nanolestes also as advanced cladotherians.[5] In a 2022 study of cladotherian relationships, it was recovered as a member of
Zatheria, closer to Theria than either Palaeoxonodon and Nanolestes.[6]