In this work, we report a neutron diffraction study on a single crystal of the layered PrBaMn2O6 perovskite. This compound undergoes two consecutive magnetic transitions with decreasing temperature. At TC ≈ 309 K, a long-range ferromagnetic ordering is established with the Mn magnetic moments oriented along the c axis. Below TN ≈ 240 K, a spin reorientation gives rise to a sudden decrease of the magnetization and the formation of an antiferromagnetic order. This magnetic transition is also accompanied by an electronic localization caused by a structural phase transition from a high-temperature tetragonal phase (P4/mmm) into a low-temperature orthorhombic one (P21am). Our neutron diffraction study at 12 K has unambiguously identified that the ground magnetic structure for this compound is a layered antiferromagnetic structure along the c axis with the Mn moments oriented in the ab plane along one diagonal of the primitive tetragonal cell. No sign of magnetic scattering associated to a CE-type magnetic structure was found in our study, discarding its occurrence in this compound. This result excludes the occurrence of a charge order transition to account for the electronic localization and it is fully consistent with previous structural studies showing a unique crystallographic site for Mn atom in the low-temperature phase. A symmetry analysis was carried out to identify the magnetic space group of the ferromagnetic order above TN and the two possible groups for the antiferromagnetic ordering below TN.