A fiber optic confocal catheter with a micro scanning lens was developed for real-time and non-contact thickness measurement of biological tissue. The catheter has an outer diameter and rigid length of 4.75 mm and 30 mm respectively and is suitable for endoscopic applications. The catheter incorporates a lens actuator that is fabricated using microelectromechanical systems (MEMS) technology. The lens is mounted on a folded flexure made of nickel and is actuated by magnetic field. Thickness measurements are performed by positioning the catheter in front of the tissue and actuating the lens scanner in the out-of-plane direction. A single-mode optical fiber (SMF) is used to deliver a 785 nm laser beam to the tissue and relay back the reflected light from the tissue to a photomultiplier tube (PMT). When the focal point of the scanning lens passes tissue boundaries, intensity peaks are detected in the reflecting signal. Tissue thickness is calculated using its index of refraction and the lens displacement between intensity peaks. The utility of the confocal catheter was demonstrated by measuring the cornea and skin thicknesses of a mouse. Measurement uncertainty of 8.86 µm within 95% confidence interval has been achieved.