A control circuit for inductive levitation micro-actuators was developed in this research, the circuit’s performance and its electrical parameters are discussed. The developed control circuit was fabricated on a four-layer printed circuit board (PCB) board with a size of 60 × 60 × 25 mm. It consisted of a generator based on high-speed Flip-Flop components and a current amplifier build on a H-bridge configuration. The circuit was able to generate an AC current with a squared waveform in a frequency range from 8 to 43 MHz and with a peak-to-peak amplitude of up to 420 mA. To demonstrate the efficiency of developed circuit and its compatibility with a micro-actuation system, an inductive levitation micro-actuator was fabricated by using 3D micro-coil technology. The device was composed of two solenoidal coil designs, a levitation and a stabilization coil, with outer diameters of 2 and 3.8 mm, respectively. A 25 μm diameter gold wire was used to fabricate the coils, with the levitation coil having 20 turns and the stabilization coil having 12 turns, similar to the micro-structure presented previously by our group. Using the developed control circuit, the micro-actuator was successfully excited and it demonstrated the actuation of aluminum disc-shaped micro-objects with diameters of 2.8 and 3.2 mm and, for the first time, an aluminum square-shaped object with a side length of 2.8 mm at a frequency of 10 MHz. To characterize the actuation, the levitation height and the current amplitude were measured. In particular, we demonstrated that the square-shaped micro-object could be lifted up to a height of 84 μm with a current of 160 mA. The characterization was supported by a simulation using a 3D model based on the quasi-finite element model (FEM) approach.