The present study examined the validity of the factor structure and invariance of the Controlling Teacher Behaviours Scale (CTBS) across two nations. Data were collected from Estonian (n = 453) and Lithuanian (n = 431) students using the multidimensional measure of teachers' controlling behaviours. Multi-sample confirmatory factor analyses showed that the measure of teachers' controlling behaviours with four scales (negative conditional regard, controlling use of rewards, excessive personal control and intimidation) were partially invariant at the configural, metric and strong invariance level. The results of the latent mean estimates showed no differences between Estonian and Lithuanian students in respect of the perception of the use of reward, whereas the perception of negative conditional regard, intimidation and excessive personal control appeared to be higher for Estonian students. The results indicated that CTBS is generally suitable for measuring the perceptions of teachers' controlling behaviour among Estonian and Lithuanian students. Furthermore, results established that one item was perceived differently across samples and, therefore, there is a need for further research to test the invariance of the CTBS among student samples with different cultural backgrounds.