This study examined changes in academic motivation among elementary and junior high school students. Based on self-determination theory (Ryan & Deci, 2000a), we focused on changes in autonomous and controlled motivation. In Study 1, we examined inter-individual changes in academic motivation among 5th to 9th grade students (N = 1 572) through a cross-sectional study. In Study 2, we examined intra-individual changes in academic motivation among students (N = 128) who were in transition from elementary to junior high school through a longitudinal study. All participants completed the Academic Motivation Scale (Nishimura, Kawamura, & Sakurai, 2011) that measured autonomous and controlled motivation. The results revealed that autonomous motivation decreased in the students from elementary to junior high school, while controlled motivation increased during the same period. This is a unique finding because a prior study conducted in a Western culture suggested that both motivations decrease gradually in school.