School absenteeism is a major social problem that can lead to poorer educational outcomes, including school dropout and social exclusion. To prevent school non-attendance and dropout, more knowledge of how absenteeism affects well-being and educational pathways in the long term is needed. This study examined the consequences of the developmental trajectories of school absences during basic education in students’ educational paths and well-being in early adulthood. The sample included 1,823 Finnish students (T1, mean age 12.76 years; 954 boys). Results revealed that students in the increasing school absences trajectory were more likely to have police contact and less likely to feel lonely. High levels of school absences and low affective engagement in upper secondary education, as well as a higher likelihood of receiving social assistance in early adulthood, were typical of the early started school absences trajectory. Parental and teacher support were protective factors against dropout intentions in upper secondary education and adverse well-being consequences in early adulthood. These results suggest that identifying and supporting students with chronic and high levels of school absences is important to reduce the risk of school dropout and poor subsequent well-being.