The analysis of rare earth elements (REEs) across beneficiation processes and in final concentrates is analytically challenging due to wide compositional variability, complex mineralogy, matrix effects, and inter-element spectral interferences. While wet-chemical, inductively coupled plasma (ICP), and X-ray fluorescence (XRF) techniques are commonly applied, XRF is often limited to process control rather than primary analysis. This is largely due to the lack of suitable calibration standards, certified reference materials, and limited specialist XRF expertise. Accurate XRF analysis requires calibration standards that adequately represent the range of matrices and concentration levels encountered in REE processing. In this work, a suite of 25 synthetic calibration standards was developed to replicate the compositional diversity present across REE beneficiation flow sheets. These standards were specifically designed for borate fusion sample preparation for XRF analysis. A dedicated REE wavelength-dispersive XRF (WD-XRF) application was established, incorporating more than 50 analytical and auxiliary fluorescence lines with optimised background correction. The method corrects for over 200 spectral overlaps and, combined with an inter-element matrix correction model, provides linear calibration over wide concentration ranges—from several hundred ppm to tens of per cent—for 44 analytes. The approach performs consistently across silicate-, clay-, and carbonate-rich ores, intermediate beneficiation products, and high-grade REE concentrates. It is also applicable to mineral sands with elevated Ti and/or Zr, as well as Ba-, Ta-, and Nb-rich materials relevant to critical minerals processing. Method accuracy and trueness were validated using commercially available certified reference materials, demonstrating analytical performance comparable to established wet-chemical and ICP based techniques. Limits of quantification typically fall within 200–400 ppm, depending on the element. Borate fusion sample preparation offers reduced environmental impact and lower operating costs compared with conventional analytical workflows. The method is readily transferable between laboratories and can be combined with pressed-pellet WD-XRF techniques to achieve detection limits of a few ppm for selected elements.