This paper reports a new and simple flow injection analysis with chemiluminescence (CL) system for determination of quercetin through the reverse flow injection technique. The method was based on the inhibition of the CL of H2O2–luminal-permanganate with quercetin. The reverse flow was used to avoid continuous monitors of CL which leads to unstable baseline. Various parameters associated with this flow system were studied and essential optimizations were carried out. Two calibration graphs were constructed for determination of quercetin in the range (6.0–12 μg/ml) with correlation coefficient (0.9994) for low concentration level and (20–190 μg/ml) with correlation coefficient (0.9962) for high concentration and a sampling frequency 80 samples/h. Possible interferences were studied and the results showed that the interferences caused less than 5% error. The method was applied successfully for the determination of quercetin in various natural products.