The Pd2HgSe3 phase was synthetized from individual elements by the silica glass tube technique and its crystal structure has been refined by the Rietveld method. The Pd2HgSe3 phase crystalizes in P$\bar 3$m1 space group with the unit-cell parameters a = 7.3096(2) Å, c = 5.2829(1) Å, V = 244.45(1) Å3, Dc = 8.84 g/cm3, and Z = 2. In its layered crystal structure, the [PdSe6] octahedra share opposing Se–Se edges with adjacent [PdSe4] squares forming layers parallel with the (001) plane. The layers show AA type stacking along the c-axis. Hg atoms occupy the anti-cubooctahedral voids between two consecutive layers. Pd2HgSe3 is isostructural with Pt2HgSe3 and Pt4Tl2X6 (X = S, Se, or Te) phases. The structure can be viewed as a 2a.2a.c superstructure of PtSe2.