The crystal structure of naturally occurring zaccariniite (RhNiAs) has been studied in Transmission Electron Microscopy (TEM) with variable angle Precession Electron Diffraction (PED) techniques. The analysis of the data has yielded tetragonal cell parameters of 3.86, 3.86, 6.77 Å and space group of P4/nmm for the basic structure, and its constituent atom positions for Ni, As and Rh were determined as well by ab-initio structure resolution method. The data is related to "Structural characterization and ab-initio resolution of natural occurring zaccariniite (RhNiAs) by means of Precession Electron Diffraction" (Roqué Rosell et al., 2019).