We developed an ultracompact three-dimensional (3D) endoscopic scanner that utilizes an electromagnetic-based stereo imaging method (EBSIM) for shape measurements. The method was used to investigate the applicability of imaging fiber optics to featureless surface profiles in confined spaces. The EBSIM is combined with a coherent flexible fiber bundle for structured light pattern projection to ensure that the scanner head can achieve a final diameter of merely 3.4 mm and a baseline length of 1.4 mm. Compared with the existing methods, the scanner is designed to have a minimum focal distance of 2 mm to address the intraoperative evaluation problem. System registration and complex calibration are unnecessary before measurements, and the scanner can be operated from any position and orientation. The scanner is capable of acquiring 3D videos at 30 frames per second. The experimental results demonstrate the feasibility of using the EBSIM for 3D surface profile measurements of featureless cylindrical surfaces. A prototype scanner is presented in extensor, and the average error of a series of known depth distances is found to be equal to 0.15 mm. The implementation shows that the 3D scanner can be potentially applied for endoscopic inspections and intraoperative evaluations in minimally invasive surgeries.