A novel thymine-containing chitosan derivative has been designed, synthesized, and used for the first time in this work for removal of some commercial pesticides from synthetic wastewater by coagulation/flocculation. The chitosan-thymine conjugate was characterized by H-1 NMR and FT-IR spectroscopy, and its flocculation performance was evaluated by UV-Vis spectroscopy in comparison to non-modified chitosan. The commercial pesticides used in this investigation were Fastac 10 EC and Karate Zeon (with alpha-Cypermethrin and lambda-Cyhalothrin, respectively, as active pyrethroid ingredients), Novadim Progress (Dimethoate as active organophosphoric ingredient), and Bordeaux mixture. The experimental results demonstrate good removal efficiency for Karate Zeon (between 80 and 85%), a maximum of around 90% for Fastac 10EC and Novadim Progress, and more than 95% for the Bordeaux mixture, irrespective of the polycation structure. According to the zeta potential values recorded in the optimum dose interval, the flocculation of pyrethroid pesticides particles took place mainly by means of the charge neutralization mechanism (close to zero), whereas the flocculation of Novadim Progress and Bordeaux mixture particles has been achieved by the synergistic effect of charge neutralization and hydrogen bonding (Novadim Progress) or copper ion binding by the amine and thymine groups (Bordeaux Mixture) (negative values).