The aim of this study is to investigate the effect of the pilates movement education program on development of flexibility and balance of the children at special education and rehabilitation centre. 28 Students (18 male + 10 female) participated to this study. The age of the students was between 8 and 16 years. Two groups were created for the research. The first group was the experimental group and consisted of 14 (9 male + 5 female) students. Second group was control group and consisted of 14 (9 male + 5 female) students. It was considered the age, gender, and physical appearance and IQ levels of the students when creating the groups. The research data analysed by SPSS 16.0 software. Pre–test and Post–test comparisons, minimum and maximum values were tabulated. According to survey results, there is no significant improvement the flexibility of the control group and a significant improvement seen the flexibility (p<0,05) of the experimental group. There is also seen a significant improvement the balance (p<0,01) of both groups. As a result, it has been observed that pilates movement education program contributes to the physical characteristics and balance skills of the children with learning difficulties.