In this article, finite element analysis and fabrication of a horn-type megasonic waveguide for nanoparticle cleaning is carried out. To design the megasonic system, the impedance graph of the megasonic waveguide is analyzed using the finite element method software ANSYS. The predicted antiresonance frequency of the piezoelectric actuator used in the system is 1003 kHz, which agrees well with the measured value of a manufactured piezoelectric actuator 1005 kHz. In addition, the antiresonance frequency of a quartz waveguide with the lead zirconate titanate actuator is predicted as 1001 kHz, which also agrees well with the experimental data of 1003 kHz. Acoustic analysis to predict the acoustic pressure distribution of the waveguide is performed, and well distributed pressures in water is observed at the end of the waveguide. Also, the acoustic pressure of the developed quartz waveguide is measured and compared with that of a commercial megasonic system having 1 MHz operating frequency. The quartz waveguide system provides a 25% more acoustic pressure output. In addition, the standard deviation is decreased by 27%. Finally, a particle removal efficiency test shows over 91% particle removal after cleaning. These results suggest that the horn-type megasonic waveguide can be applied to the nanoparticle cleaning process.