Whole grain wheat flour is valued for its nutritional and antioxidant properties due to its high levels of phenolic compounds. However, its high bran content can negatively impact dough handling, bread texture, and colour, posing a challenge for developing healthier baked products with desirable sensory qualities. While sieving is commonly used to separate bran from endosperm, little is known about how controlled flour fractionation at specific particle sizes (250 µm and 500 µm) affects the distribution of bioactive compounds and flour functionality. Hence, this study investigated the impact of flour fractionation by sieving (250 µm and 500 µm) on colour, water absorption capacity, total phenolic content (TPC), total flavonoid content (TFC), antioxidant activity (2,2-diphenyl-1-picrylhydrazyl [DPPH] and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) [ABTS]), and selected phenolic compound composition. Whole white wheat flour (WWF) and whole brown wheat flour (BWF) were included for comparison. BWF showed the highest water absorption (0.84 mL/g), while fractionated flours (0.65–0.69 mL/g), particularly the 250 µm fraction, demonstrated improved lightness and higher TPC (approx. 3.2 mg QE/g) compared to BWF (1.39 mg QE/g) and WWF (1.97 mg QE/g). Although BWF retained higher antioxidant activity, fractionation significantly influenced phenolic compound profiles. Trans-ferulic acid was the predominant compound, and quercetin levels remained consistent across all samples. Principal component analysis (PCA) of TPC, TFC, phenolic acids, and antioxidant activities (ABTS and DPPH) explained over 75% of the total variance in the first two components, revealing distinct clustering by flour type and fraction. These findings highlight the potential of targeted flour fractionation as a novel strategy to enhance both the functional and nutritional properties of whole grain flours, offering a balanced solution for improving whole grain bread making without the need for full bran removal. Future studies should apply the flour in baked goods, including bread, muffins, and cakes.