The school must teach how to think.-Ewald Il' enkov Background. While the current literature provides valuable insight into how school climate perceptions and student motivation impact academic achievement, research examining the mediating effects of motivation in the linking of an innovative educational system, school climate, and achievement is limited. This study considers the potential of the El'konin-Davydov system of developmental education as a basis for educational innovation. Self-determination theory is applied as a useful theoretical framework that allows for consideration of both the intensity and the quality of academic motivation. Objective. The study examines a model that illustrates the role of intrinsic and different types of extrinsic motivation in linking the El'konin-Davydov system of developmental education (DE) and school climate to the academic achievement of elementary schoolchildren. Design. Participants were 345 third and fourth graders drawn from four public schools in Moscow, with some (N = 192, 2 schools) educated in the traditional system and others (N = 153, 2 schools) in one that follows the DE system. A cross-sectional design was implemented. Results. Students in the DE system showed significantly lower external motivation for all three subscales (Parents, Teachers, General) and perceived school climate more favorably. Structural equation modeling showed that the hypothesized model fit the data well, supporting the hypothesis that student external motivation plays a mediating role in linking educational system (innovative vs. traditional) with academic achievement. Students' autonomous motivation was shown to play a mediating role in linking positive perceptions of school climate with academic achievement.