Pierini, P. Operating the Third Harmonic SRF System in the E-XFEL Injector JACoW Geneva, Switzerland The E-XFEL injector was commissioned and operated with beam in 2016. Part of the injector is a third harmonic system of 8 SRF cavities operating at 3.9GHz. This paper describes all aspects of the commissioning and operation of the third harmonic system with beam.