To collect the signals of magnetic nanoparticles (MNPs) at a distance from a magnetic nanoparticle tomography, a strong ac magnetic field should be generated by applying a high current to the excitation coil. To this end, sinusoidal excitation using a linear amplifier-type ac power source has been applied to the tomography. Although this source can provide a high-quality sinusoidal voltage, its low power efficiency is not suitable for generating the required high current. To overcome this limitation, we use an H-bridge voltage source inverter to achieve high efficiency by generating a square-wave voltage. However, the third harmonic component in the square wave, undermines the acquisition of MNP signals. Thus, we suppress the third harmonic by shifting the switching phase of the inverter transistors. As a result, the third harmonic in the excitation current is reduced to less than one-tenth of that obtained after conventional suppression. We verify the distribution of MNP signals at depths up to 50 mm using the proposed excitation approach. The results demonstrate the effectiveness of the proposed approach based on square-wave inverter excitation for magnetic nanoparticle tomography.