A simple, disposable and inexpensive electrochemical DNA biosensor based on a zirconia (ZrO2) modified thin film screen-printed electrode (ZrO2/SPE) has been developed. Short DNA sequences (21 monomer units) from the Escherichia coli pathogen, modified with a phosphate group at the 5′ end, were attached to the surface of the electrode through the affinity of the phosphate group for zirconia, to produce an effective DNA probe (ssDNA/ZrO2/SPE). DNA immobilization and hybridization were characterized using differential pulse voltammetry by employing methylene blue as redox indicator. Target sequences hybridized with the probe resulted in a decrease of the reduction peak current of methylene blue intercalated into the probe. The response of a non-complementary sequence and a single base pair mismatch sequence were both clearly distinguished from that of a complementary sequence. The developed biosensor had a high selectivity and sensitivity towards hybridization detection (10–10 M complementary DNA detectable). Making use of screen-printed technology, the fabrication of the biosensors exhibited satisfactory reproducibility, investigated by cyclic voltammetry and differential pulse voltammetry. The relative standard deviation was found to be <3.0% for six bare SPEs and six ssDNA-modified SPEs (ssDNA/ZrO2/SPE) from a batch.