Bioretention system is a new and green ecosystem to regulate the urban surface runoff and water quality purification, but its removal efficiency for perfluorinated compounds is unknown. Based on the reported concentrations of perfluorinated compounds in surface runoff, two cylindrical bioretention systems were constructed with traditional fillers mixed with 2~4 mm zeolite (volume ratio of 10%) or 2~4 mm improved coal granular activated carbon (volume ratio of 10%) as the main fillers. The removal efficiencies of conventional contaminants and perfluorinated compounds by both systems were investigated, as well as the one-year operation efficiency. The results showed that the water reduction rate decreased with the extension of operation time, and the average reduction rate was (29.8±8.2)%. After one-year operation, the average removal rates of COD, TN, TP, TOC and NH⁺₄-N by the bioretention column with the improved coal granular activated carbon were 67.49%, 84.78%, 76.43%, 80.28% and 65.43%, respectively, which were better than bioretention column with zeolite. The removal efficiencies of PFPeA, PFHxA, PFHpA, PFOA, PFOS and PFNA maintained above 80%. The spatial distribution of pollutants showed that PFBA was mainly concentrated in the plant layer, while PFPeA, PFHxA, PFHpA, PFOA, PFOS and PFNA were concentrated in the filler layer.