Pulsating high gradient magnetic separation (PHGMS) for removing trace amounts of iron impurities from a quartz ore was investigated using a lab-scale PHGMS separator, and its performance was further confirmed through a pilot-scale PHGMS separator. The results of this investigation indicated that PHGMS is effective for removing the iron impurities from the ore. By applying the lab-scale separator with a rod matrix of 1.5 mm diameter to the ore containing 0.063% Fe2O3, a concentrate assaying 0.0079% Fe2O3 with 89.82% iron removal rate was achieved through a two-step purification of PHGMS. It was found that the separation performance of this lab-scale separator was closely correlated with the wire diameter of matrix, pulsating frequency and background magnetic induction. Compared with the separation characteristics of PHGMS in beneficiating feebly magnetic metallic ores, it is clear that a much gentler pulsating intensity and a much higher background magnetic induction are both required to maintain a high iron removal rate. The comparison test of HIWGS further evidences the positive effect of pulsating energy in the high gradient magnetic separation. The purification performance of the lab-scale separator was well duplicated by the pilot-scale one, so that it was concluded that PHGMS provides an effective way for removing trace amounts of iron impurities from similar non-metallic ores.