Electrochemical detection is the simplest analytical tool to be integrated into digital microfluidics (DMF). It offers the advantages of small size, with detector electrodes incorporated into the device by patterning, and high compatibility with portable analytical instruments. Indium tin oxide (ITO) coated on glass has been commonly used for the top plate of DMF due to its good conductivity and transparency. However, instability and the low current response of ITO electrodes patterned on glass hindered their application for immunoassays. It has been reported that ITO coated on polyethylene terephthalate (PET) has better conductivity, owing to its higher carrier concentration, faster mobility and lower resistivity. Herein, we investigated the use of ITO electrodes patterned on PET film as the top plate of DMF for a simple and stable electrochemical immunoassay using square wave voltammetry (SWV), with an excellent peak resolution and high sensitivity. A magnetic bead-based immunoassay for H5N1 antigen was performed on a DMF platform with a limit of detection of 0.6 ng mL−1 in buffer and 18 ng mL−1 in human serum. These results showed the good electrochemical performance of ITO coated on a PET film, a lightweight, shock resistant and cost-effective material, which is promising for DMF fabrication and transparent electrodes for various electroanalytical methods.