A miniature microwave electron cyclotron resonance plasma source [(discharge diameter)/(microwave cutoff diameter) < 0.3] has been developed at Kyushu University to be used as an ion thruster in micro-propulsion applications in the exosphere. The discharge source uses both radial and axial magnetostatic field confinement to facilitate electron cyclotron resonance and increase the electron dwell time in the volume, thereby enhancing plasma production efficiency. Performance of the ion thruster is studied at 3 microwave frequencies (1.2 GHz, 1.6 GHz, and 2.45 GHz), for low input powers (<15 W) and small xenon mass flow rates (<40 μg/s), by experimentally measuring the extracted ion beam current through a potential difference of ≅1200 V. The discharge geometry is found to operate most efficiently at an input microwave frequency of 1.6 GHz. At this frequency, for an input power of 8 W, and propellant (xenon) mass flow rate of 21 μg/s, 13.7 mA of ion beam current is obtained, equivalent to an calculated thrust of 0.74 mN.