Transition from primary to secondary school is more successful when students’ learning is consistent. Students are also more likely to enjoy the school, engage with learning, and have a high academic achievement in the secondary school when they feel motivated. This is a critical aspect especially in cases when global pandemics situations allow only the online schooling opportunity. Students that are away from school lack the traditional sources of motivation and self-regulated learning skills, thus research is needed to identify other important factors that can be developed in remote settings. The aim of this study was to find out how students perceive their experience with the transition from primary to secondary school and how such a transition influences students’ self-regulated learning (SRL) and motivation. Self-reported data were collected during the COVID-19 breakout from a total of N=80, 6th and 7th grade students aged 12-14 years old. Results showed that students had a successful transition, especially when they are supported by their parents and teachers. Next, Bivariate Pearson Correlation analysis indicated that students’ perceptions about their experience with the transition from primary to secondary school and their self-regulated learning and motivation are significantly correlated. No gender differences were found among all main study variables.