Neutron resonance transmission technique was applied for assaying isotopic fissile materials produced in the pyro-process. In each process of the pyro-process, a different composition of the fissile material is produced. Simulation was basically performed on 235U and 239Pu assay for TRU-RE product, hull waste, and uranium addition. The resonance energies were evaluated for uranium and plutonium in the simulation, and the linearity in the detection response was examined on the fissile content variation. The linear resonance energies were determined for the analysis of 235U and 239Pu on the different fissile materials. For enriched TRU-RE assay, the sample condition was suggested; The sample density, content, and thickness are the key factors to obtain accurate fissile content. The detection signal is discriminated for uranium and plutonium in neutron resonance technique. The transmitted signal for fissile resonance has a direct relation with the content of fissile. The simulation results indicated that the neutron resonance technique is promising to analyze 235U and 239Pu for various types of the pyro-process material. An accurate fissile assay will contribute toward safeguarding the pyro-processing system.