Cyberbullying perpetration (CBP) and problematic Internet use (PIU) are the most studied risky online activities for adolescents in the current generation. However, few studies have investigated the relationship between CBP and PIU. Still lacking is a clear understanding of common or differentiated risk and protective pathways for adolescents interacting in the cyber world. The aim of this study was to understand the role of individual (emotional symptoms) and environmental variables (parental monitoring) underpinning both CBP and PIU, with time spent online as a mediator of these factors. Furthermore, we investigated gender and school level differences in these dynamics. A questionnaire was filled in by 3,602 students from Italian Lower Secondary Schools and Upper Secondary Schools. Structural equation modeling was used to test the effects of emotional symptoms and parental monitoring on CBP and PIU mediated by time spent online, controlling for school level. In addition, the model was implemented for girls and boys, respectively. Negative emotional symptoms and low levels of parental monitoring were risk factors for both CBP and PIU, and their effect was mediated by the time spent online. In addition, parental monitoring highlighted the strongest total effect on both CBP and PIU. Risk and protective pathways were similar in girls and boys across Lower Secondary and Upper Secondary Schools, although there were some slight differences. CBP and PIU are the outcomes of an interplay between risk factors in the individual and environmental systems. The results highlight the need to design interventions to reduce emotional symptoms among adolescents, to support parental monitoring, and to regulate the time spent online by adolescents in order to prevent risky online activities.