Excessive foot pronation has been reported as being related to chronic low back pain symptoms and risk factors in sports-specific pathologies. Compensating custom-made foot orthotics treatment has not been entirely explored as an effective therapy for chronic low back pain (CLBP). This study aims to observe the effects of custom-made foot orthoses, in subjects with foot pronation suffering from CLBP. A total of 101 patients with nonspecific CLBP and a pronated foot posture index (FPI) were studied. They were randomized in two groups: an experimental one ( = 53) used custom-made foot orthotics, and the control group ( = 48) were treated with non-biomechanical effect orthoses. The CLBP was measured using the Oswestry Disability Index (ODI) Questionnaire and a visual analogue scale (VAS), both for lower back pain. The symptoms were evaluated twice, at first when the subject was included in the study, and later, after 4 weeks of treatment. The analysis of outcomes showed a significant decrease in CLBP in the custom-made foot orthoses participants group ( < 0.001 ODI; < 0.001 VAS). These findings suggest that controlling excessive foot pronation by using custom-made foot orthoses may significantly contribute to improving CLBP.