The transition from primary to secondary school is more successful when students’ learning is consistent. Students are also more likely to enjoy school, engage with learning, and have a high academic achievement in secondary school when they feel motivated. This is a critical aspect, especially in cases in which global pandemic situations allow only online schooling opportunities. 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 sixth and seventh grade students aged 12–14 years old. The results showed that students had a successful transition, especially when they were 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, their self-regulated learning, and their motivation were significantly correlated. No gender differences were found among any of the main study variables. Teachers can foster students’ SRL skills by implementing effective teaching methods and by guiding them towards SRL-enhancing techniques.