Radioisotope irradiators (using cesium-137 or cobalt-60) are used as sources of ionizing radiation to control quarantine or phytosanitary insect pests in internationally traded fresh commodities and to sterilize insects used in sterile insect release programs. There are institutional initiatives to replace isotopic irradiators (producing γ-rays) with lower-energy X-ray machines due to concerns about radiological terrorism and increasingly stringent regulations on the movement of radioisotopes. Questions remain about whether the biological effects of low-energy X-rays are comparable to those of γ-rays since differences in energy levels and dose rates of X-rays may have different efficacies. We compared adult emergence, flight ability, and adult survival in the Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritdae), after irradiation of third instar larvae with 100 kV or 5 MeV (5,000 kV) X-rays at 20 and 40 Gy in replicated studies. At 20 Gy, the adult emergence rate was significantly lower after irradiation with 100 kV compared to 5 MeV X-rays, suggesting higher efficacy at the lower energy level. In a follow-up study using 100 kV X-rays, applying 20 Gy using a slow dose rate (0.24 Gy min^–1) resulted in significantly higher adult emergence than did a fast dose rate (3.3 Gy min^–1), suggesting lower efficacy. Although our study suggests higher efficacy of low energy 100 kV X-rays, there is uncertainty in measuring the dose from an X-ray tube operating at 100 kV using an ionization chamber; we discuss how this uncertainty may change the interpretation of the results. Using a 100 kV X-ray irradiator to develop a phytosanitary treatment may underestimate the dose required for insect control using commercial high-energy γ-ray or X-ray systems.