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Removal of pharmaceutically active compounds (PhACs) is of great importance in wastewater reclamation due to their potent negative impact on human health. Typical polyamide nanofiltration (NF) membranes are negatively charged, which compromises their rejection rate of positively charged PhACs. Herein, we propose to rationally design a novel thin-film nanocomposite (TFN) NF membrane featuring dually charged metal organic framework (MOF) to effectively remove both positively and negatively charged PhACs. Ethylenediamine (ED) was grafted to the coordinately unsaturated metal sites inside the MIL-101(Cr). The resulting ED-MIL-101(Cr) contained both amine groups inside its channels to provide strong positive charge and negatively charged carboxyl groups at its surface. This dually charged nature of the MOF nanoparticles enabled the ED-MIL-101(Cr)-containing TFN membrane to achieve high rejection rates (mostly >90%) for both positively (terbutaline, atenolol, fluoxetine) and negatively charged PhACs (ketoprofen, diclofenac, bezafibrate). At the same time, the ED-MIL-101(Cr) TFN membrane had greatly improved water permeance (140% over the control membrane with MOF loading). Calculations based on density functional theory further confirmed the large energy barrier for the migration of both negatively and positively charged PhACs across the nanochannels of ED-MIL-101(Cr). This study highlights a promising potential of dually charged MOF-TFN membranes for efficient removal of trace organic contaminants in wastewater reclamation.