Antibiotic resistance has been recognized as a major threat to public health worldwide. Inactivation of antibiotic resistant bacteria (ARB) and degradation of antibiotic resistance genes (ARGs) are critical to prevent the spread of antibiotic resistance in the environment. Conventional disinfection processes are effective to inactivate water-borne pathogens, yet they are unable to completely eliminate the antibiotic resistance risk. This study explored the potential of the photo-Fenton process to inactivate ARB, and to degrade both extracellular and intracellular ARGs (e-ARGs and i-ARGs, respectively). Using Escherichia coli DH5α with two plasmid-encoded ARGs (tetA and blaTEM-1) as a model ARB, a 6.17 log ARB removal was achieved within 30 min of applying photo-Fenton under visible LED and neutral pH conditions. In addition, no ARB regrowth occurred after 48-h, demonstrating that this process is very effective to induce permanent disinfection on ARB. The photo-Fenton process was validated under various water matrices, including ultrapure water (UPW), simulated wastewater (SWW) and phosphate buffer (PBS). The higher inactivation efficiency was observed in SWW as compared to other matrices. The photo-Fenton process also caused a 6.75 to 8.56-log reduction in eARGs based on quantitative real-time PCR of both short- and long amplicons. Atomic force microscopy (AFM) further confirmed that the extracellular DNA was sheared into short DNA fragments, thus eliminating the risk of the transmission of antibiotic resistance. As compared with e-ARGs, a higher dosage of Fenton reagent was required to damage i-ARGs. In addition, the tetA gene was more easily degraded than the blaTEM-1 gene. Collectively, our results demonstrate the photo-Fenton process is a promising technology for disinfecting water to prevent the spread of antibiotic resistance.