Background: The study of injuries stemming from sacroiliac dysfunction in athletes has been discussed in many papers. However, the treatment of this issue through thrust and muscle-energy techniques has hardly been researched. The objective of our research is to compare the effectiveness of thrust technique to that of energy muscle techniques in the resolution of sacroiliac joint blockage or dysfunction in middle-distance running athletes. Methods: A quasi-experimental design with three measures in time (pre-intervention, intervention 1, final intervention after one month from the first intervention) was made. The sample consisted of 60 adult athletes from an Athletic club, who were dealing with sacroiliac joint dysfunction. The sample was randomly divided into three groups of 20 participants (43 men and 17 women). One intervention group was treated with the thrust technique, another intervention group was treated with the muscle–energy technique, and the control group received treatment by means of a simulated technique. A prior assessment of the range of motion was performed by means of a seated forward flexion test, a standing forward flexion test, and the Gillet test. After observing the dysfunction, the corresponding technique was performed on each intervention group. The control group underwent a simulated technique. A second intervention took place a month later, in order to ascertain possible increased effectiveness. Results: Statistically significant differences were found between the muscle energy technique (MET) and muscle energy groups compared with the placebo group in both interventions (p = 0.000), with a significant reduction in positive dysfunction (initially 20 in all groups, eight in MET group, and two in thrust group in the final intervention). Comparing the changes in time, only the thrust group obtained statistically significant differences (p = 0.000, with a reduction of positive dysfunction, starting at 20 positives, five positive in the initial intervention and two positive in the final intervention) and when comparing both techniques, it was observed that between the first intervention and the final intervention, the thrust technique was significantly higher than the MET technique (p = 0.032). Conclusions: The thrust manipulation technique is more effective in the treatment of sacroiliac dysfunction than the energy muscle technique, in both cases obtaining satisfactory results with far middle-distance running athletes. Finally, the thrust technique showed positive results in the first intervention and also in the long term, in contrast to the MET technique that only obtained changes after the first intervention.