The title compound, [PdBr2(C21H13F5N2)2], crystallizes with two independent centrosymmetric conformational isomers having a square-planar coordination at the Pd atom. The conformational isomers differ by the ligands having a cis or trans orientation of their benzyl and pentafluorobenzyl rings with respect to the benzimidazole ring plane. The benzimidazole rings are rotated with respect to the coordination plane of the metal by 79.1 (2) and 75.2 (1) degrees for molecules A and B, respectively. The Pd-Br bond lengths are 2.4218 (8) and 2.4407 (10) A for molecules A and B, respectively, and the Pd-C bond lengths are 2.030 (8) and 2.018 (9) A. The crystal structure contains two types of C-H...F and one type of C-H...Br intramolecular contact, as well as C-H...pi interactions.