In this paper, EMI measurement, the STGU simulation being conducted, filter design, its characteristics, and its implementation to the PCB, and finally test results are discussed. When the low pass filter was implemented within the STGU, the power of EMI decreased more than 20dBm. Finally, when TE and MTIE, two important quality measure in synchronous reference clock, was assessed, ITU-T G813 requirement was satisfied. EMI(Electromagnetic Interface) is a measure of electomagnetic radiation from equipment in the range of 10KHz to 3GHz, and can cause unexpected reactions of electronics/electrical equipment. In this study, for safe and stable communication operation, a STGU (System Timing Generation Unit), which is a 2.5G SDH System and a major EMI source, was employed to simulate electromagnetic interface. Using Open-Site test, the power of fundamental frequency of EMI of interest and its harmonics were measured. Also, a low pass filter at cut-off frequency of 2GHz was specifically designed for this study to minimize the effect of EMI between electronic components.