Objectives: The study aimed to assess the effectiveness of a health education-based training program in enhancing the level of health empowerment among refugees in Jordan. Health empowerment is a crucial component of health promotion, enabling individuals to take control of their health, manage their health outcomes, and improve them. Refugees are a vulnerable population group with limited access to healthcare. Methods: The study sample consisted of 38 refugees in Irbid governorate, Jordan, who were conveniently selected in coordination with some organizations working in the field of asylum in the governorate. They were randomly divided into two groups: an experimental group (n = 19) that received the health education training program, and a control group (n = 19) that did not receive any health education training. The Health Empowerment Scale (HES), a validated tool, was used to collect data from both groups in pre-tests and post-tests, and a follow-up test was conducted for members of the experimental group only. Results: The results showed a statistically significant increase in the health empowerment scores for the experimental group that received the training program compared to the control group. The mean of the pre-test for the experimental group was (1.97 ± 0.27), and for the control group, it was (1.84 ± 0.21). The post-test mean for the experimental group became (3.88 ± 0.13), while for the control group, it was (1.85 ± 0.20). The follow-up test indicated sustained enhanced levels of health empowerment in the experimental group, with little difference between the post-test and follow-up scores, indicating the effectiveness of the health education training program in enhancing health empowerment for refugees in Jordan. Conclusions: Healthcare providers and policymakers in Jordan and other countries hosting large numbers of refugees have significant responsibilities. Giving sufficient priority to health education and awareness programs is essential to enhance the health empowerment of refugees and improve their health literacy, which ultimately impacts their overall public health.