Abstract Background Sickness absence is associated with lower school achievements and early school leaving. The Medical Advice for Sick-reported Students (MASS) intervention is a proactive school-based intervention focused primarily on early identification and reduction of sickness absence. This study used a program evaluation framework to evaluate the MASS intervention among intermediate vocational education students and Youth Health Care professionals. Outcome indicators were primarily number of sick days, education fit, and school performance, and secondarily, seven health indicators. Process indicators were dose delivered and received, satisfaction, and experience. Methods The MASS intervention evaluation was conducted in ten intermediate vocational education schools. Students with extensive sickness absence from school in the past three months were included in either the intervention or control condition. Students completed a baseline and a six-month follow-up self-report questionnaire. Linear and logistic regression analyses were applied. Students and Youth Health Care professionals completed an evaluation form regarding their satisfaction and experience with the intervention. Results Participants (n = 200) had a mean age of 18.6 years (SD = 2.02) and 78.5% were female. The MASS intervention showed positive results on decreasing sickness absence in days (β = -1.13, 95% CI = -2.22;-0.05, p < 0.05) and on decreasing depressive symptoms (β = -4.11, 95% CI = -7.06;-1.17, p < 0.05). No effects were found for other health indicators (p > 0.05). A significant interaction revealed a decline in sickness absence in males (p < 0.05) but not in females (p > 0.05). Youth Health Care professionals found the application of the MASS intervention useful (n = 35 forms). The mean rating of students for the consultation within the MASS intervention was an 8.3 (SD = 1.3) out of 10 (n = 14 forms). Conclusions Our study provides some indication that the MASS intervention has positive effects on decreasing both sickness absence and depressive symptoms among intermediate vocational education students. The Youth Health Care professionals who provided the consultation as part of the MASS intervention considered the intervention to be useful and stated that the consultation was delivered as intended in almost all cases. Students were generally satisfied with the intervention. We recommend that future research evaluates the MASS intervention in a large randomized controlled trial with a longer follow-up. Trial registration This study was prospectively registered in the Netherlands Trial Register under number NTR5556, in October 2015.