We present an electrostatic microelectromechanical systems (MEMS) resonant scanner with large out-of-plane translational stroke for fast axial-scanning in a multi-photon microscope system for real-time vertical cross-sectional imaging. The scanner has a compact footprint with dimensions of 2.1 mm × 2.1 mm × 0.44 mm, and employs a novel lever-based compliant mechanism to enable large vertical displacements of a reflective mirror with slight tilt angles. Test results show that by using parametrical resonance, the scanner can provide a fast out-of-plane translational motion with ≥400 μm displacement and ≤0.14° tilt angle over a wide frequency range of ~390 Hz at ambient pressure. By employing this MEMS translational scanner and a biaxial MEMS mirror for lateral scanning, vertical cross-sectional imaging with a beam axial-scanning range of 200 μm and a frame rate of ~5–10 Hz is enabled in a remote scan multi-photon fluorescence imaging system.