We introduce a novel electrochemical method for the purification of complex water-soluble functional polymers contaminated with copper salts originating from copper-catalyzed azide/alkyne ligation chemistry, for which no standard purification protocol is suitable. A triethylene glycol methyl ether methacrylate (TEGMA) star polymer with 2-ureido-4H-pyrimidone (UPy) end groups was prepared via an activator generated by electron transfer atom transfer radical polymerization (AGET ATRP) and copper-catalyzed azide/alkyne cycloaddition (CuAAc) and selected as a model system for electrolysis of an aqueous polymer solution. We systematically investigate the influence of sample concentration, voltage, and time of electrolysis on the quality of the purification. Atom emission spectroscopy (AES) reveals almost quantitative removal of copper, and size exclusion chromatography (SEC) as well as proton nuclear magnetic resonance spectroscopy (1H NMR) ensure the full integrity of the polymer under all selected conditions.