Background: Research has shown that the teacher-student interpersonal relationship (TSIR) is important for student motivation. Although TSIR has received a growing interest, there are only few studies that focus on changes and links between TSIR and student academic motivation in a longitudinal fashion in non-Western contexts. Aims: This study investigated changes in TSIR and links with academic motivation as perceived by first-grade secondary school students in Indonesia. TSIR was studied from the perspective of interpersonal behaviour in terms of Influence and Proximity. Students' academic motivation was studied from the perspective of self-determination theory. Sample and methods: A total of 504 first-grade secondary school students of 16 mathematics and English classes participated in the study. Surveys were administered in five waves throughout the school year. Multilevel growth curve modelling was applied. Results: Contrary to the (limited) general research findings from Western contexts, we found that the quality of TSIR (student perceptions) increased over time. The increase was slightly more pronounced for Proximity than for Influence. In accordance with the findings for the Western countries, the level of students' controlled motivation increased, while that of autonomous motivation decreased over time. However, the negative change in autonomous motivation was less pronounced. As in Western countries, TSIR was longitudinally linked with academic motivation, in particular, with autonomous motivation. Conclusions: Evidence is found that TSIR can change in a favourable way, and this positively affects student motivation. Future research could benefit from unravelling the influences of cultures on changes in TSIR in broader contexts.