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Graphene quantum dots (GQDs) have received great attention as optical agents because of their low toxicity, stable photoluminescence (PL) in moderate pH solutions, and size-dependent optical properties. Although many synthetic routes have been proposed for producing GQD solutions, the broad size distribution in GQD solutions limits its use as an efficient optical agent. Here, we present a straightforward method for size fractionation of GQDs dispersed in water using a cross-flow filtration system and a track-etched membrane with cylindrical uniform nanopores. The GQD aqueous suspension, which primarily contained blue-emitting GQDs (B-GQDs) and green-emitting GQDs (G-GQDs), was introduced to the membrane in tangential flow and was fractionated with a constant permeate flow of about 800 L m−2 h−1 bar−1. After filtration, we observed a clear blue PL spectrum from the permeate side, which can be attributed to selective permeation of relatively small B-GQDs. The process provided a separation factor (B-GQDs/G-GQDs) of 0.74. In the cross-flow filtration system, size-dependent permeation through cylindrical nanochannels was confirmed by simulation. Our results demonstrate a feasible method facilitating size fractionation of two-dimensional nanostructures using a cross-flow membrane filtration system. Since membrane filtration is simple, cost-effective, and scalable, our approach can be applied to prepare a large amount of size-controlled GQDs required for high performance opto-electronics and bio-imaging applications.