Josephson junction plays a key role not only in studying the basic physics of unconventional iron-based superconductors but also in realizing practical application of thin-film based devices, therefore the preparation of high-quality iron pnictide Josephson junctions is of great importance. In this work, we have successfully fabricated Josephson junctions from Co-doped BaFe2As2 thin films using a direct junction fabrication technique which utilizes high energy focused helium ion beam (FHIB). The electrical transport properties were investigated for junctions fabricated with various He+ irradiation doses. The junctions show sharp superconducting transition around 24 K with a narrow transition width of 2.5 K, and a dose correlated foot-structure resistance which corresponds to the effective tuning of junction properties by He+ irradiation. Significant J c suppression by more than two orders of magnitude can be achieved by increasing the He+ irradiation dose, which is advantageous for the realization of low noise ion pnictide thin film devices. Clear Shapiro steps are observed under 10 GHz microwave irradiation. The above results demonstrate the successful fabrication of high quality and controllable Co-doped BaFe2As2 Josephson junction with high reproducibility using the FHIB technique, laying the foundation for future investigating the mechanism of iron-based superconductors, and also the further implementation in various superconducting electronic devices.