Phase synchronization measures are widely used for investigating inter-regional functional connectivity (FC) of brain oscillations, but which phase synchronization measure should be chosen for a given experiment remains unclear. Using neuromagnetic brain signals recorded from healthy participants during somatosensory stimuli, we compared the performance of four phase synchronization measures, imaginary part of phase-locking value, imaginary part of coherency (ImCoh), phase lag index and weighted phase lag index (wPLI), for detecting stimulus-induced FCs between the contralateral primary and ipsilateral secondary somatosensory cortices. The analyses revealed that ImCoh exhibited the best performance for detecting stimulus-induced FCs, followed by the wPLI. We found that amplitude weighting, which is related to computing both ImCoh and wPLI, effectively attenuated the influence of noise contamination. A simulation study modeling noise-contaminated periodograms replicated these findings. The present results suggest that the amplitude-dependent measures, ImCoh followed by wPLI, may have the advantage in detecting stimulus-induced FCs.