High-frequency transformers are the core components of power electronic transformers (PET), whose insulation is deeply threatened by high voltage (HV) and high frequency (HF). The partial discharge (PD) test is an effective method to assess an electrical insulation system. A PD measurement platform applying different frequencies was set up in this manuscript. PD signals were acquired with a high-frequency current transducer (HFCT). For improving the signal-to-noise (SNR) ratio of PD pulses, empirical mode decomposition (EMD) was used to increase the SNR by 4 dB. PD characteristic parameters such as partial discharge inception voltage (PDIV) and PD phase, number, and magnitude were all analyzed as frequency dependent. High frequency led to high PDIV and a smaller discharge phase region. PD number and magnitude were first up and then down as the frequency increased. As a result, a suitable frequency for evaluating the insulation of high-frequency transformers is proposed at 8 kHz according to this work.