Optical-resolution photoacoustic microscopy (OR-PAM) is a novel microscopic tool to provide in vivo optically sensitive images in biomedical research. Conventional OR-PAM systems are typically slow and bulky because of the linear scanning stages with stepping motors. For practical purposes, however, fast imaging speed and small footprint are crucial. To address these issues, we have developed a real-time compact OR-PAM system equipped with a waterproof two-axis MEMS scanner. The OR-PAM system consists of key components such as an ultrasonic transducer with a bandwidth of 50 MHz, an opto-acoustic beam combiner (BC), and an MEMS scanner. These are all installed inside a small water tank, with dimensions of 30 mm × 90 mm × 30 mm along the x-, y-, and z-axes, respectively. A pulsed laser with a repetition rate of 50 kHz is confocally aligned with the photoacoustic (PA) waves in the BC to maximize the SNRs. The fast scanning ability of the MEMS scanner fully utilizes the A-scan speed of 50 kHz. For instance, the B- and C-scan imaging speeds are 125 Hz and 0.625 Hz, respectively, when the acquired PA maximum amplitude projection image has 200 × 200 pixels along the x- and y-axes, respectively. The measured lateral resolution of 3.6 μm and axial resolution of 27 μm are sufficient to resolve the small capillaries. Finally, we have successfully obtained in vivo PA images of iris microvasculatures in mice. This real-time and compact OR-PAM system is optimized to examine small animals in clinical studies.