The effects of radiofrequency (RF) heating on the activity, structure, and surface hydrophobicity of mushroom polyphenol oxidase (PPO) were examined and four kinetic models of inactivation (First-order model, Weibull model, Logistic model and Bi-phasic model) were fitted. The results demonstrated that RF heating could effectively inactivate PPO, logistic and Bi-phasic model attained the best fit. The circular dichroism (CD) and fluorescence spectroscopy spectra revealed that RF heating at 65 °C for 180 s caused changes in the secondary and tertiary structures of PPO, reducing the α-helix content from 38.5% to 30.3% and red-shifting the emission peak wavelength of the maximum fluorescence intensity from 318 nm to 321 nm. RF heating also caused a significant enhancement of the surface hydrophobicity of the PPO (P < 0.05). The color test results showed that RF heating could inhibit the browning of mushrooms (P < 0.05). Thus, RF heating is an effective technique for the inactivation of enzymes and further research should be performed on RF heating applications to inactivate enzymes in the food industry.