The transition to secondary education is a sensitive period for social and academic development and also for student identity. However, there is scarce evidence of the development of reading comprehension and theory of mind in pupils with cochlear implant (CI) during the educational trajectory. The results show that pupils with CI obtain age-appropriate reading scores during the educational transition. Theory of mind development seems to be heterogeneous in CI users and be affected after the educational transition compared to their own performance in the first wave. This variability could be related to adaptation to secondary education and their individual characteristics.