In this paper, a rapid and sensitive flow injection‐chemiluminescence (FI‐CL) method is proposed for the quantitative determination of rutin based on the inhibitory effect of rutin on the chemiluminescence intensity from the luminol–chymotrypsin (CT) system. The decrease of CL intensity was found to be proportional to the logarithm of rutin concentration in the range 0.1–30.0 ng/mL. A method for the quantification of rutin is proposed, with the limit of detection (LOD) of 0.03 ng/mL (3σ). A complete analytical process including sampling and washing for rutin determination, which was conducted at a flow rate of 2.0 mL/min, could be performed completely within 30 s, yielding a sample efficiency of 120 h−1. The proposed procedure was successfully applied for the determination of rutin in human urine after oral intake, with recoveries varying from 93.9 to 108.1% and relative standard derivation <4.0% (n = 5). Results showed that urine reached the maximum concentration at ~2.5 h, and the total excretion ratios were (83.5 ± 0.6) and (86.8 ± 0.7)%, respectively, for two volunteers in 8 h. The pharmacokinetic parameters, including the half‐life (1.05 ± 0.02 h), absorption rate constant (1.18 ± 0.01 h−1), and elimination rate constant (0.70 ± 0.01 h−1), were obtained. The possible CL mechanism of the luminol–CT–rutin reaction is discussed by FI‐CL, fluorescence, and molecular docking methods.