Introduction: Handball is one of most associated sports with low back injuries. Low back pain is one of the main reasons for physical incapacity among athletes, with a negative impact on training and competition [1]. Clinical pilates uses minimal loads to improve trunk activation and endurance, aiming to improve posture and movement control through the strengthening of the core, leading to the decrease of low back pain [2,3]. The goal of this study was to verify the benefits on low back pain, through the application of a clinical pilates program, during six weeks, in young handball players of the youth team, junior and senior, of the Ginásio Clube do Sul. Materials and methods: This study included 18 male, athletes with lumbar pain from training overload existing for more than 3 months. The subjects were, randomized into two groups: experimental group (EG) and control group (CG). The EG performed a clinical Pilates program before the usual handball weekly workouts and the control group performed only the usual handball weekly workouts, and they were given a flyer with trunk strengthening and postural control exercises. The study lasted six weeks, with evaluation moments at week 0 (M0) and in the end of week 6 (M1). The study was approved by Ginásio Clube do Sul and all participants gave their informed consent. Results: Both groups were homogeneous regarding participants age (19.66 ± 2.85 vs 19.61 ± 2.96) and weight (80.78 ± 7.35 vs 80.58 ± 5.43). In the mean values, athletes in the EG had lower values than the CG in functional disability (2.1 ± 1.5 vs 3.25 ± 1.75) and pain score (3 ± 1.5, vs 4.25 ± 0.7), and higher values for endurance of the trunk (flexors - 73.9 ± 24.5, extensors - 75.3 ± 24.7, right lateral flexors - 41.1 ± 26.5, left lateral flexors - 43.35 ± 26.8; ± 24.1, vs flexors 56.1 ± 24.1, extensors- 63.2 ± 15.6, right lateral flexors- 32.8 ± 16.1, left lateral flexors- 35.5 ± 19.2). Within groups, we could see statistically significant differences in the functional disability variable (p = 0.02), pain intensity (p = 0.03) and endurance in the trunk flexors (p = 0.04) and extensors (p = 0.01) for the EG, from M0 to M1; In CG, there are no statistically significant differences except from pain intensity (p = 0.04). The functional disability and pain intensity value decreased from M0 to M1 in the EG with a moderate to high effect. The value of endurance of trunk flexors and extensors increase from M0 to M1 with a moderate to high effect. Discussion and conclusion: Clinical Pilates has benefits on handball athletes with low back pain, leading to a decrease in pain intensity and functional incapacity, as well as an increase in the endurance of the trunk flexors and extensors. Despite clinical Pilates have promising effects controling pain symptomatology, functional capacity and endurance of the trunk in young Handball athletes, further investigation with larger sample is needed.