Magnetic noise of a two-stage pulse tube cryocooler (PT) was measured by a fundamental mode orthogonal fluxgate magnetometer and by a LTS Double Relaxation Oscillation SQUID (DROS) first-order planar gradiometer. The magnetometer was installed in a dewar made of aluminum at 12cm distance from a section containing magnetic regenerative materials of the second pulse tube. The magnetic noise spectrum showed a clear peak at 1.8Hz, which is the fundamental frequency of the He gas pumping rate. The 1.8Hz magnetic noise registered a peak, during the cooling down process, when the second cold-stage temperature was around 12K, which is well correlated with the 1.8Hz variation of the temperature of the second cold stage. Hence, we attributed the main source of this magnetic noise to the temperature variation of the magnetic moments resulting from magnetic regenerative materials, Er 3 Ni and HoCu 2 , in the presence of background static magnetic fields. We have also pointed out that the superconducting magnetic shield of lead sheets reduced the low frequency magnetic noise generated from the magnetic regenerative materials. With this arrangement, the magnetic noise amplitude measured with the LTS DROS gradiometer, mounted at 7cm horizontal distance from the magnetic regenerative materials, in the optimum condition, was lower than 500pT peak-to-peak, whereas the noise level without lead shielding was higher than the dynamic range of DROS instrumentations which was around ±10nT.