Pulse tube (PT) cryocoolers can be used to cool SQUIDs, however their electromagnetic interference (EMI) through the conducted high frequency noise currents are normally too large to operate SQUIDs. In this paper, high frequency noise currents of a pulse tube cryocooler system are simultaneously observed at several critical points to analyze conducting paths of the noise currents and to find a solution for this problem. High frequency noise currents are detected by current sensors consisting of a current transformer and a terminating resistor at the secondary side. By covering three-phase power lines and a neutral line connecting the valve motor to the inverter with a copper mesh, and by using it as an additional neutral line, conducted EMI (noise currents) to the cryostat has bee reduced by one fifth. With this treatment, SQUIDs have been operated normally.