AbstractAn (ICP‐OES) based analytical methodology was developed for the determination of metallic constituents (Al, Ca, Co, Cr, Cu, Fe, Ga, In, Mn, Mg, Na, Ni, Si, V, W and Zn) at minor and trace level in U−Mo alloy fuel after preferential separation of emission rich major matrix using TBP‐HDBO‐NTf2 without any compromise on the determination of analytes at trace levels. Application of ionic liquid, HDBO‐NTf2 drastically reduced the time of analysis (30 min reduction per sample) and generation of toxic organic waste (20 mL per sample) containing U and Mo. The method was optimized by identification of analytical lines of the elements free from spectral interference of U and Mo, establishing the calibration curves using those lines and evaluation of analytical performances (detection limit, linear dynamic range etc.) in U−Mo matrix. The preferential separation of U and Mo were found to follow anion exchange and cation exchange mechanism involving UO2((NO)3)3.2TBP− and MoO2(NO3) TBP+ species, respectively, which differ in their conventional separation by solvation mechanism involving ML2 and ML1 neutral species, respectively. Preferential separation by HDBO‐NTf2 based system can be effectively used for determination of analytes of 10 ppm concentration at 10 % error limit. The total uncertainty in estimation of each analyte have been estimated. The real sample analyses data were compared to that obtained by n‐dodecane based ICP‐OES method and direct analysis of Energy Dispersive X‐ray Fluorescence spectroscopic (EDXRF) method. The data were found to be in good agreement with each other. The experimentally obtained results were subjected to t‐test with 95 % confidence limit and 10 degrees of freedom. The texpt was found to be less than tcrit 2.228 revealing reliability of the methods. The experimentally obtained variance values (Fexpt) were found to be less than Fcrit∼2.980 revealing the variance values are within acceptable statistical error limit.