The disease brought about by the SARS-CoV-2, COVID-19 coronavirus has had an unprecedented global impact. Confinement to control the outbreak may have mental health consequences for the most vulnerable in the population, including adolescents. This study aims to describe and analyze the relationships between the stress variables, Emotional Intelligence and the intention to use cannabis in healthy adolescents, before and after the end of the COVID-19 pandemic containment stage. A comparative correlational study was carried out with validated self-completed questionnaires through an online platform. The sample is made up of adolescents (n = 300) aged 13–17 from two different schools in Ponferrada (León, Spain). The analysis of correlation and differences between the groups indicate that confinement has had effects on the mental health of the adolescents, specifically on the emotional manifestations of stress. Furthermore, significant gender differences were found for stress values and Emotional Intelligence. However, no differences have been found for cannabis use intention.