Background: Unhealthy eating habits are a major problem among adolescents. The objective of the study was to assess the effect of a free breakfast club intervention on dietary habits among students at vocational schools. Methods: The study included students (n = 318) from four vocational schools in Denmark. Food frequency questionnaires were used to measure eating habits at baseline, first, and second follow-up, after 7 and 14 weeks respectively, in a clustered randomized controlled intervention of four months. The effect of the intervention was evaluated through self-reported frequencies of breakfast intake, intake of whole grain products for breakfast and intake of unhealthy snacking in the morning. The outcome measures were daily breakfast intake (yes/no), daily intake of whole grain for breakfast (yes/no), and unhealthy snacking on school day mornings (yes/no). Results: The proportion of students who had breakfast every school day increased significantly in the intervention schools from baseline to the first follow-up compared to the control group (OR: 3.77; P = 0.0149). The effect was attenuated at the second follow-up. The intake of whole grain products for breakfast increased significantly more among students in intervention schools compared to students in control schools both at first (OR: 4.13; P = 0.0079) and second follow-up (OR: 3.27; P = 0.0317). No significant change in unhealthy snacking was found. Conclusion: Provision of free breakfast at vocational schools can improve the dietary quality of breakfast and decrease breakfast skipping. However, the sustainability of the intervention is a critical issue that needs to be further studied and addressed. Trial registration: ISRCTN11265280. Registered 20 November 2018 (retrospectively registered).