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The ordered perovskite compound Ba2PrRuO6 is prepared and its magnetic properties are investigated. The Rietveld analysis of the neutron diffraction profiles measured at 150 K shows that the Pr3+ and Ru5+ ions are arranged with regularity over the six-coordinate B sites of the perovskite ABO3 and that Ba2PrRuO6 belongs to space group P21/n, with a = 6.0063(5), b = 5.9863(4), c = 8.4677(7) Å and 90.04(2)°. The magnetic susceptibility and the heat capacity measurements show that this compound transforms to an antiferromagnetic state below 117 K. From the neutron diffraction patterns measured at 7 K, the magnetic structure is determined to be of Type I and the magnetic moments of Pr3+ and Ru5+ are estimated to be 2.2(1) and 2.0(2) µB, respectively. Their values are discussed on the basis of theoretical calculations for the crystal field splitting.