This research aims to find out the implementation of single sex education class and co-education in grade XII science program of SMA Muhammadiyah Bantul and the different learning achievement of students in single sex education class and co education in grade XII science program of SMA Muhammadiyah Bantul. This is a qualitative study using field research. Meanwhile, descriptive qualitative was used as the approach of the research. Thus, this research is a comparative study. The findings of the research show that the implementation of single sex education class in XII science class was MBS class, while the co education was regular class. The students’ learning achievement of single sex education class was higher than that of co education class. It happened because single sex education was a class inhabited by the students of MBS program-Islamic based boarding school. In addition, the treatment done in this class lead to a better learning environment, so the teaching and learning process was more conducive. Meanwhile, the students’ learning achievement of co education class was lower caused by the disturbed students’ concentration in learning. The students especially the male ones were easily distracted by the female students. This disturbance also made the female students could not focus well during the teaching and learning process.