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The water contamination from pharmaceuticals and personal care products (PPCPs) has attracted worldwide attention in recent years because of its threat to public health. Berberine is a typical anti-inflammatory medicine and berberine wastewater is difficult to be treated due to its high toxicity, poor biodegradability, and high acidity. Metal–organic frameworks would be a good choice to remove berberine from wastewater due to its advantages of high specific surface area, ultrahigh porosity, and structural and functional tunability. In this study, MIL-101­(Fe) was synthesized and used for the removal of berberine from water. Experimental results indicated that MIL-101­(Fe) showed promising characteristics when berberine was adsorbed in acidic wastewater. The high concentration of chloride in berberine wastewater could promote the adsorption of berberine by MIL-101­(Fe). Fitting of batch equilibrium data showed that MIL-101­(Fe) had a maximum adsorption capacity of 163.93 mg/g for berberine removal at pH 7, and the berberine sorption on MIL-101­(Fe) followed the pseudo-second-order model. Furthermore, the associate mechanism for berberine removal was proposed by characterizing the material and theoretical calculation. The X-ray power diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS) analysis showed that no chemical reaction occurred during the adsorption of berberine by MIL-101­(Fe). Also, the theoretical calculation results indicated that π–π interactions may play the main role in the adsorption of berberine onto MIL-101­(Fe). The findings of this study suggest that MIL-101­(Fe) is a promising sorbent for berberine removal from wastewater.