Topological antiferromagnetic spintronics is an emerging field due to advantages such as no stray field effect and high-speed dynamics. In bismuth chalcogenide topological insulators, the coexistence of long-range antiferromagnetic order and topologically protected states has scarcely been observed. Here, an antiferromagnetic order, which sets in the direction of magnetic moments perpendicular to the c axis, is introduced by Eu substitution in Bi2Se3, and therefore it influences the topological electronic properties of Bi2Se3. Despite Eu substitution, Shubnikov–de Haas (SdH) oscillations are observed. The angle dependence of SdH oscillations shows a signature of anisotropic 3D Fermi surfaces with a nontrivial Berry phase by Eu substitution, and the temperature dependence of SdH oscillations reveals that the effective mass is comparable to the pristine Bi2Se3. These results suggest that the nontrivial topological state can survive in the antiferromagnetic order of Eu-substituted Bi2Se3. Our work expands the base of topological materials available for antiferromagnetic spintronics applications.