Purpose <p>The current study aims to optimize an RP-HPLC method for the simultaneous estimation of iguratimod (IGU) and methotrexate (MTX) using a quality-by-design (QbD) approach and to validate it in accordance with ICH Q2(R2).</p> Methods <p>The method was developed based on QbD principles using a 4-factor 2-level full-factorial design (2⁴ FFD). The analysis was performed on a ZORBAX Eclipse Plus C18 column (4.6 × 250&#xa0;mm, 5&#xa0;μm). The estimation of IGU and MTX was performed using a mobile phase of acetonitrile and orthophosphoric acid buffer (pH 3.0) in gradient mode at a flow rate of 1.0 mL/min. The detection was performed at the isosbestic wavelength of 276&#xa0;nm. A forced degradation study (acid/base hydrolysis, heat, light, UV radiation) was performed to identify degradation pathways and products. The greenness assessment was done using AGREEprep and AGREE tools. The method was applied to determine the drug content of iguratimod and methotrexate in the Self-Emulsifying Drug Delivery System.</p> Results <p>The retention times for methotrexate and iguratimod were obtained at 4.4 and 6.9&#xa0;min, respectively. The developed RP-HPLC method demonstrated linearity over 0.4–6.0&#xa0;µg/mL (R² = 0.9999), as well as precision, accuracy, selectivity, and robustness. The limit of detection (LOD) and limit of quantification (LOQ) for methotrexate were 12.19 ng/mL and 36.94 ng/mL, respectively. For iguratimod, these limits were 30.24 ng/mL and 91.65 ng/mL, respectively. The developed method was identified as a green method based on AGREEprep (0.63) and AGREE (0.64) scores.</p> Conclusion <p>The study concludes that the developed method is precise, accurate, simple, robust, and environmentally friendly. This is useful for the simultaneous estimation of iguratimod and methotrexate in lipid-based formulations and other pharmaceutical dosage forms.</p> Graphical Abstract <p></p>