It is expected that ion trap quantum computing can be made scalable through protocols that make use of transport of ion qubits between sub-regions within the ion trap. In this scenario, any magnetic field inhomogeneity the ion experiences during the transport, may lead to dephasing and loss of fidelity. Here we demonstrate how to measure, and compensate for, magnetic field gradients inside a segmented ion trap, by transporting a single ion over variable distances. We attain a relative magnetic field sensitivity of Delta B/B_0 ~ 5*10^{-7} over a test distance of 140 micro m, which can be extended to the mm range, still with sub micro m resolution. A fast experimental sequence is presented, facilitating its use as a magnetic field gradient calibration routine, and it is demonstrated that the main limitation is the quantum shot noise.
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