OBJECTIVE: To investigate the effects of an exercise program, based on the Pilates Matwork method, on posterior chain flexibility and trunk mobility in healthy school age children. DESIGN AND SETTING: The study was a parallel-group randomized clinical trial. The participants were randomly assigned to groups: Pilates Group (PG) and Control Group (CG). The program was developed at the Early Childhood Education Institute, Londrina-PR. PARTICIPANTS: 43 children with age between eight to 12 years, no prior knowledge of the Pilates method, and no exercise training in the last six months. INTERVENTION: Four months of twice a week 50 min Pilates Matwork exercises were administered. OUTCOME MEASURES: Flexibility and mobility, assessed using the sit-and-reach test, fingertip-to-floor test and photogrammetry. The assessors were blinded to the allocation of participants. RESULTS: Three children were excluded before randomization and 40 were randomized (PG n = 20; CG n = 20).12 children were excluded during the protocol (PG n = 7; CG n = 5) and included in the intention to treat analysis. No significant difference between groups was observed for flexibility measures. There was a significant difference in the following outcomes for the PG: distance reached in the sit-and-reach test between pre-test (median 14.25[11.25-28.38]) and post-test (median 20.25[12.00-29.63]) (ES = 0.29, SRM = 0.73); Posterior angle of the knee in the fingertip-to-floor test between pre-test (median 191.60[187.20-191.60]) and post-test (median 189.00[185.90-191.50]) (ES = 0.56, SRM = 0.54). CONCLUSION: There were no differences in posterior chain flexibility and trunk mobility between school age children who underwent Pilates Matwork exercises and the control. However, children who participated in the exercise program showed improvement in some results of flexibility. CLINICAL TRIAL REGISTRATION NUMBER: Brazilian Registry of Clinical Trials (REBEC) (N° RBR-8t5p7d).