Abstract We present the result of searching for clusters of galaxies based on weak gravitational lensing analysis of the ∼160 deg2 area surveyed by Hyper Suprime-Cam (HSC) as a Subaru Strategic Program. HSC is a new prime focus optical imager with a 1${^{\circ}_{.}}$5-diameter field of view on the 8.2 m Subaru telescope. The superb median seeing on the HSC i-band images of 0${^{\prime\prime}_{.}}$56 allows the reconstruction of high angular resolution mass maps via weak lensing, which is crucial for the weak lensing cluster search. We identify 65 mass map peaks with a signal-to-noise (S/N) ratio larger than 4.7, and carefully examine their properties by cross-matching the clusters with optical and X-ray cluster catalogs. We find that all the 39 peaks with S/N > 5.1 have counterparts in the optical cluster catalogs, and only 2 out of the 65 peaks are probably false positives. The upper limits of X-ray luminosities from the ROSAT All Sky Survey (RASS) imply the existence of an X-ray underluminous cluster population. We show that the X-rays from the shear-selected clusters can be statistically detected by stacking the RASS images. The inferred average X-ray luminosity is about half that of the X-ray-selected clusters of the same mass. The radial profile of the dark matter distribution derived from the stacking analysis is well modeled by the Navarro–Frenk–White profile with a small concentration parameter value of c500 ∼ 2.5, which suggests that the selection bias on the orientation or the internal structure for our shear-selected cluster sample is not strong.