Abstract: In fusion experiments, the integrators are fundamental instruments to recover differential signals from magnetic probes. The conventional analog integrators are single-ended input, which have low common mode rejection ratio (CMRR). A kind of difference integrator was developed which has the same structure as the standard difference amplifier in this paper. The principles of the integration for difference input signal and rejection for common mode signal were analyzed. A zeroing circuit was designed to reduce the integration drift. The test results show that this kind of difference integrator works well with stable and adjustable integration drift, when the common voltage is 1.5 V, its integration drift in 100 s is 80 μWb, and its CMRR is up to 125 dB, which is much better than single-ended integrator. The difference integrators were successfully used for flux loop measurement with the anti-series connection in 2012 Experimental Advanced Superconducting Tokamak (EAST) campaign.