Matrix certified reference materials (CRMs) play a critical role in analytical method validation and the assurance of reliable measurement results. A certified reference material (GBW(E)100813) for whole-wheat flour was developed to ensure an accurate and reliable measurement of the main Fusarium mycotoxins (deoxynivalenol (DON), nivalenol (NIV), deoxynivalenol-3-glucoside (DON-3G), and zearalenone (ZEN)). CRM candidates were prepared using sun-drying, grinding, sieving, homogenising, packaging, and gamma irradiation. The final produced CRM was packaged at 50 g per unit and stored at 20 °C. Certification was performed using isotope dilution-liquid chromatography–tandem mass spectrometry. CRM characterization was performed in eight laboratories in accordance with the requirements of ISO Guide 35. The certified values and expanded uncertainties (at a confidence of 95%, k = 2) for DON, NIV, DON-3G, and ZEN were determined to be 0.98 ± 0.12 mg/kg, 1.37 ± 0.20 mg/kg, 242 ± 35 μg/g, and 382 ± 50 μg/g. The CRM was sufficiently homogeneous between and within bottles, and remained stable for up to 12 months at 20 °C and 9 days below 40 °C for transportation. Thus, CRM can be used for quality control and method validation to ensure the accurate and reliable quantification of the main Fusarium mycotoxins in whole-wheat flour.