A new ultrasonic reactor was used to rapidly inactivate Escherichia coli and Staphylococcus aureus in apple juice. It was found that high pulp content made ultrasound less lethal to S. aureus, while it had no significant effect on E. coli. When the pulp free apple juice was ultrasonically processed, the 5-log reduction time was 35 s for E. coli at 60 °C and 30 s for S. aureus at 62 °C. Ultrasound treatment had no significant effect on antioxidant activity determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, but it significantly increased the total phenolic content. The treatment also resulted in more stable juice with higher uniformity. During 28 d of storage at 4 °C, the total plate count in apple juice ultrasonically treated at 60 °C for 35 s remained around 1.00 log CFU/mL, whereas it was nearly zero for a stronger ultrasound treatment at 62 °C for 30 s. These values were much lower than those in the untreated one, which increased from 3.65 log CFU/mL to 8.36 log CFU/mL during the storage. At the end of the storage, the control and thermally treated apple juice lost almost 70% of antioxidant activity, whereas the ultrasonically treated juice only lost 20–40%.