Securing the safeguardability of a reprocessing process for spent nuclear fuels (SNFs) is imperative. Particularly, the quantity of special nuclear materials inside SNFs must be estimated with the highest achievable precision. Unlike aqueous reprocessing, pyro-processing involves handling input materials in a solid state. Hence, partially extracted samples analyzed by destructive assay (DA) should maintain an acceptable level of representativeness. In this study, a representative sampling method widely applied in the pharmaceutical industry was adopted for homogenization in the head-end process of pyro-processing. By employing representative sampling, specifically based on the mechanism of the rotary riffler, the overall process of homogenization prior to DA analysis was simplified, and less probable hold-up that could contribute to materials unaccounted for (MUF) would be expected. The resulting Pu sampling uncertainty was confirmed to be less than 1% (for ≥ 1,000 μm particle size and ≤ 5 kg sample mass), ensuring sufficient control of Pu accounting uncertainty at a reasonably low level (≤ 1%). Thus, representative sampling can be a competitive alternative to previously suggested methodologies.