During the COVID-19 outbreak, the imposition of home restriction or quarantine led to the use of emergency remote teaching for education purposes. Adolescent students faced a challenge while trying to maintain a school experience and receive reliable information about the pandemic. This study presents the results for students’ perceptions of teaching, social and cognitive presence and the relationships between them, as described in the CoI framework, during the implementation of emergency remote teaching. Data derived from the answers of 47 junior high school students to the CoI survey, after attending online courses that incorporated both asynchronous and synchronous distance learning tools. Results show that teaching presence is significantly and positively correlated to social presence and cognitive presence. Starting from the high correlation between teaching and cognitive presence, simple regression analysis was used in order to calculate a model for predicting cognitive presence.