The COVID-19 pandemic has negatively affected educational settings (ES) in Slovenia. To effectively limit the emergence and spread of SARS-CoV-2 infections in ES, it is important to identify the pathways of introduction and transmission of infection. This study aims to analyse the spread of infections in ES according to the level of education, taking into account the predominant variant of the virus in Slovenia in order to advise on public health action. We calculated the incidence rate of infection by age group, according to the level of the ES. Additionally, we analysed data on the reported outbreak criteria in ES. In Slovenia, SARS-CoV-2 infections in children and adolescents (1–18 years) accounted for 16.8% of all confirmed infections. The incidence and leading outbreak criteria differed according to the level of the ES and predominant SARS-CoV-2 variant. The occurrence of cases in ≥3 different “bubbles” was the most common outbreak criteria (59%). A high number of employee-imported outbreaks was observed in pre-school settings (44%). As countries move away from widespread nonpharmaceutical interventions, the focus should be on vaccination promotion among teaching staff in pre-school settings and systemic solutions, such as self-testing and ventilation, to enable safe educational environments.