The intention of this study was to find the learning trajectory of two-variable linear equations system in Junior High School. This study was design research using validation study. The participants of this study were Junior High School students in grade IX SMPIT Luqman al-Hakim Yogyakarta Indonesia. Data were collected through observation and interview. Data were analysed using Milles & Huberman model. Result revealed that the learning trajectory of the two-variables linear equation system were to deepen the mastery of algebra and one-variable linear equation system, model the two-variable linear equation system, solve the experiments, complete the two-variable linear equation using graphs, complete two-variable linear equations by substitution, simple elimination, complex elimination, and mixed method, and solve two-variable linear equation system problems. Keywords: learning trajectory, two-variable linear equation system, design research.