INTRODUCTION: Helicopter pilots may present chronic low back pain due to vibration exposure and asymmetric posture during flight. OBJECTIVES: To analyze the effects of a Pilates-based exercise program on low back pain of helicopter pilots of the Brazilian Air Force. METHODS: This is a randomized controlled trial with fifteen helicopter pilots of the Brazilian Air Force, who were assessed for pain intensity (Numerical Pain Rating Scale), disability associated with low back pain, and spine muscle endurance in three positions: trunk extension (Ito test) and left and right lateral bridge. Individuals were randomly distributed into the regular exercises group (REG) (n = 7), oriented to maintain their exercise routine, and Pilates group (PG) (n = 8), which performed an exercise program based on Pilates method twice a week for 12 weeks. Reassessments occurred after 6 and 12 weeks. Data were analyzed on SPSS 20.0 software using a significance level of 5%. RESULTS: PG showed a significant reduction in low back pain after 12 weeks of training compared with REG (mean difference of 3.5 points, p < 0.0001). We also observed increased endurance of trunk extensors (p = 0.002) and right (p = 0.001) and left lateral muscles (p = 0.001) in the PG compared with REG. However, the indexes of disability did not change between groups. CONCLUSION: Pain intensity was significantly reduced while spine muscle endurance increased in PG compared with REG after intervention; thus, Pilates-based exercises should be considered in physical conditioning programs for helicopter pilots.