Background: School absenteeism (SA) is associated with anxiety, depression, and disruptive behavior. It is a risk factor for academic difficulties and school dropout, which predict problems in adulthood such as social, work-related, and health problems. The main goal of this study is to examine the initial effectiveness of a modular transdiagnostic cognitive behavioral therapy (CBT) intervention (Back2School) for increasing school attendance and decreasing psychological problems, relative to a comparator control arm (treatment as usual [TAU]). Methods/design: One hundred sixty children, aged 7 to 16 years, will be randomly assigned to either Back2School or TAU. The design is a two (Back2School and TAU) by four (preassessment [T1], postassessment [T2], and 3-month [T3] and 1-year [T4] assessments) mixed between-within design. The primary outcome is school attendance based on daily registration. Secondary outcomes pertain to youth psychosocial functioning, quality of life, bullying, self-efficacy, and teacher-parent collaboration. These secondary outcomes are measured via youth, parent, and teacher reports. Discussion: This study will provide critically needed empirical evidence on the initial effectiveness of a manualized treatment program for youth with SA. If the intervention is found to be effective, the program can be further implemented and tested in a larger school health effectiveness trial. Trial registration: ClinicalTrials.gov, NCT03459677. Retrospectively registered on 9 March 2018.