The electrochemical halogenation of polythiophene derivatives (PTs) such as poly(3-hexylthiophene) (PHT), poly(thiophene-alt-9,9-dioctylfluorene) (PTF) and poly(bithiophene-alt-9,9-dioctylfluorene) (PBT) was investigated using a thin-layered cell. The reactivity and the current efficiency of the electrochemical halogenation of polythiophene derivatives were markedly improved by using the thin-layered cell as compared to using a conventional beaker-type cell. Moreover, the use of the thin-layered cell reduces the amount of electrolytic solution required. In addition, the optical and electrochemical properties of the obtained polymers were significantly changed by the complete substitution of chlorine atoms onto the thiophene ring.