The main objective of this study was to assess the pesticide removal efficiency of chitosan in grape juice during clarification. The grape juice was spiked with six selected pesticides (chlorpyrifos, ethion, diazinon, fenitrothion, fenthion and phorate) and clarified with chitosan at different concentrations and at three different incubation times (1, 2 and 4 h). The effect of chitosan on the level of pesticides in grape juice during clarification was quantified using modified QuEChERS method with gas chromatography with tandem mass spectrometry (GC-MS/MS). The method for pesticide quantification has been validated. The maximum removal was obtained for chlorpyrifos (98%) and ethion (97%) at 0.5% of chitosan concentration for 1 h incubation followed by phorate (96%), fenthion (95%), fenitrothion (94%) and diazinon (86%) at 1% of chitosan concentration for 2 h incubation time. The juice was clarified with other clarifying agents such as activated carbon, gelatin, casein and bentonite and its pesticide removal efficiency was compared with chitosan. The pesticide removal level could be correlated with the properties of selected pesticides and clarifying agents. The results indicated that the chitosan can act as an effective pesticide scavenger and it leads to the potential application of chitosan in fruit juice clarification.