MnPd5Se, a derivative of the anti-CeCoIn5-type phase, was synthesized from a high-temperature solid-state reaction, structurally determined by X-ray diffraction, and magnetically characterized with a combined magnetic measurement and neutron powder diffraction (NPD). According to the X-ray diffraction results, MnPd5Se crystallizes in a layered tetragonal structure with the same space group as CeCoIn5, P4/mmm (No. 123). MnPd5Se shows antiferromagnetic ordering around 80 K on the basis of the magnetic property measurements. An A-type antiferromagnetic structure was revealed from the analysis of neutron powder diffraction results at 300, 50, and 6 K. Moreover, a spin orientation rotation was observed as the temperature decreased. Pd L3 X-ray absorption near edge spectroscopy results for MnPd5Se semiqualitatively correlate with the calculated density of states supporting a nominal 0.2 electron transfer into the Pd d orbital from either Se or Mn in the compound. The discovery of MnPd5Se, along with our previously reported MnT5Pn (T = Pd or Pt; Pn = P or As), provides a tunable system for studying the magnetic ordering from ferromagnetism to antiferromagnetism with the strong spin-orbit coupling effect.