This study evaluated the quality and safety of red dragon fruit (Hylocereus polyrhizus) juice after pasteurization by high-intensity pulsed electric fields (HIPEF) following ultrasound-assisted extraction. Ultrasound treatment was conducted at 40% amplitude for 10 minutes, followed by cold pressing. HIPEF pasteurization was applied at 40 kV/cm with a 21 μs pulse width and 600 pulses. Treated juice was compared to an untreated control, focusing on betacyanin content, total phenolic content (TPC), total flavonoid content (TFC), antioxidant activity, total soluble solids, pH, enzymatic activity (PPO and POD), and microbial counts. During refrigerated storage (4 ± 1°C) for two months, PEF-treated juice retained higher betacyanin levels. TPC initially declined but peaked at day 30, while TFC remained higher than the control for the first month before gradually decreasing. Antioxidant activity was well maintained, with 82% retention after two months. HIPEF processing significantly reduced enzymatic activities, with PPO and POD decreasing by 86.3% and 81.4%, respectively, despite minor fluctuations during storage. Microbiological evaluation showed an immediate 5-log reduction in total plate count, with minimal yeast and mold presence. Over storage, yeast and mold counts slowly increased, whereas bacterial counts declined, likely due to pitaya’s antimicrobial properties. No psychrophilic bacterial growth was detected. Overall, HIPEF pasteurization effectively preserved the juice’s quality attributes and microbial safety for up to two months under refrigeration.