Accurate near-field measurements for either deterministic or stochastic electromagnetic fields characterization require a relevant process that removes the influence of the probes, transmission lines, and measurement circuits. The main part of the experimental work presented here is related to a calibration procedure of a test setup consisting of a microstrip test structure and a scanning loop probe. The calibration characteristic, obtained by comparing measured and simulated results, is then used to convert the measured voltage into the magnetic field across and along the microstrip line at the specific height above it. By performing the measurements and simulations of the same test structure with the loop probe in the presence of an additional scanning probe, the influence of the additional probe to the measured output is thoroughly investigated and relevant corrections are given. These corrections can be important when two-point correlation measurement is required, especially in scanning points when two probes are mutually close.