The invention is related to the field of telecommunications, particularly to the optical wavelength division multiplexing (WDM) systems, where rare earth doped-fiber optical amplifiers are used. The invention is a system for a rare earth elements doped optical fiber effective area measurements with micro-positioner to get doped optical fiber effective area value by using transversal shift measurement method. Measurement system contains two light sources (1, 2), which are connected to Y type power coupler (3), after which follows micro-positioner (5) with stationary and moveable platform on which optical fiber is fixed (8), whose output is connected to an optical spectrum analyzer (9), furthermore to provide the functioning of micro-positioner (5) it is connected to a micro-positioner control unit (6) and a computer (7), as well as two microscopes (4) for visual monitoring, that are directed to the fiber being measured (8) end surface from two angles, which differ each from other by 90o.