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The objectives of this study was to determine the profile of student-s error, student-s misconception, cause of student misconception, and students learning difficulties on system of linear equation in two varibles topic. The research was carried out by giving test of concept understanding on that topic. Subject of the study were junior high school students who had studied system of linear equation in two variables topic. The results of the study revealed that there were the students error profile, six students misconception profiles, four causes of students- misconceptions, and seven causes of learning difficulties. Based on the results of the students test it was found 71% of students had difficulty in determining the solution of system of linear equations in two variables algebraic form. This indicated students had difficulty in using, utilizing, and choosing a particular procedure on this topic. In addition, from the results of teachers-s interview, it was found one of the causes students- misconception to be the inaccuracy definition of system of linear equation in two variables. Students learning difficulties were mostly derived from student learning activities at school.