We have developed a high-resolution scanning superconducting quantum interference device (SQUID) microscope for imaging the magnetic field of geological samples at room temperature. In this paper, we provide details about the scanning SQUID microscope system, including the magnetically shielded box (MSB), the XYZ stage, data acquisition by the system, and initial evaluation of the system. The background noise in a two-layered PC permalloy MSB is approximately 40–50 pT. The long-term drift of the system is approximately ≥1 nT, which can be reduced by drift correction for each measurement line. The stroke of the XYZ stage is 100 mm × 100 mm with an accuracy of ~10 µm, which was confirmed by laser interferometry. A SQUID chip has a pick-up area of 200 μm × 200 μm with an inner hole of 30 μm × 30 μm. The sensitivity is 722.6 nT/V. The flux-locked loop has four gains, i.e., ×1, ×10, ×100, and ×500. An analog-to-digital converter allows analog voltage input in the range of about ±7.5 V in 0.6-mV steps. The maximum dynamic range is approximately ±5400 nT, and the minimum digitizable magnetic field is ~0.9 pT. The sensor-to-sample distance is measured with a precision line current, which gives the minimum of ~200 µm. Considering the size of pick-up coil, sensor-to-sample distance, and the accuracy of XYZ stage, spacial resolution of the system is ~200 µm. We developed the software used to measure the sensor-to-sample distance with line scan data, and the software to acquire data and control the XYZ stage for scanning. We also demonstrate the registration of the magnetic image relative to the optical image by using a pair of point sources placed on the corners of a sample holder outside of a thin section placed in the middle of the sample holder. Considering the minimum noise estimate of the current system, the theoretical detection limit of a single magnetic dipole is ~1 × 10−14 Am2. The new instrument is a powerful tool that could be used in various applications in paleomagnetism such as ultrafine-scale magnetostratigraphy and single-crystal paleomagnetism.