Magnetic structures and the relationship between spin and charge-orbital orderings of an A-site ordered double-perovskite manganite SmBaMn2O6, an anticipated multiferroic material, were investigated by means of neutron diffraction. The spin arrangement in MnO2 planes perpendicular to the c axis is revealed to be the same as that in the A-site disordered half-doped manganites CE-type but the stacking pattern is found to be different displaying a unique twofold period. The temperature dependence of the superlattice magnetic and nuclear reflections clarifies that the antiferromagnetic spin ordering occurs at a temperature slightly lower than the temperature at which a rearrangement of the charge-orbital orderings occurs. The result evidences that the rearrangement leads the spin ordering. The intensities of the magnetic reflections are found to change across Tf = 10 K, suggesting a spin-flop by 90 [deg.] while keeping the Mn spin ordering pattern unchanged.