The article presents the results of the development of a system for measuring emittance characteristics of ion sources studied at the IAP NAS of Ukraine with the aim of obtaining the ion beams with a high brightness. The emittance measurement system is based on the scheme of an electrostatic scanner and consists of two main parts: the scanner, which moves in the direction perpendicular to the beam axis using a stepper motor, and the electronic system of control, processing and data acquisition. The electronic system contains a Raspberry pi 3B microcomputer, precision DAC/ADCs, the high-voltage amplifier of a scanning voltage up to ±500 V on deflection plates of the scanner and a wide range current integrator. The determination of the emittance consists in measuring the ion beam intensity distribution when the scanner moves along the x-coordinate and the electrostatic scanning along the x´ angle. The obtained two-dimensional data array allows determining the main characteristics of ion beam: geometric 90% emittance, the root mean square (rms) emittance, the Twiss parameters and phase ellipse of rms emittance, the beam current profile and the angle current density distribution. To test the performance and functionality of the system, the emittance characteristics of the penning type ion source were measured. The working gas was helium, and the beam energy varied within 7–15 keV. At 13 keV of beam energy the following emittances of the He+ ions beam was obtained: 90% emittance is 30 π∙mm∙mrad, rms emittance is 8.4 mm∙mrad, and the normalized rms emittance is equal to 0.022 mm∙mrad. The developed system for measuring the emittance of the ion beams is characterized by a short measurement time of 10-15 minutes.