Background The popularity of the gluten‐free diet and sales of gluten‐free products have increased immensely. Aims To investigate whether gluten induces gastrointestinal symptoms, measured by self‐reported questionnaires, as well as mental health symptoms in adolescents from a population‐based cohort. Methods The eligible participants (n = 273) were recruited from a population‐based cohort of 1266 adolescents and had at least four different gastrointestinal symptoms. Phase one (n = 54) was a run‐in phase where the participants lived gluten‐free for 2 weeks. If they improved they continued to phase 2 (n = 33), a blinded randomised cross‐over trial. Participants were blindly randomised either to start with 7 days of gluten, eating two granola bars containing 10 g of gluten or to 7 days on placebo, eating two granola bars without gluten, followed by the reverse and separated by a 7‐day washout period. The effects of the intervention on gastrointestinal symptoms and mental health symptoms were assessed. Results In total, 54/273 participants entered the run‐in phase and 35 were eligible for randomization. A total of 33 were randomised and 32 completed the trial. The median age was 20.3 (IQR 19.2–20.9) and 32/33 participants were females. Compared with a placebo, gluten did not induce gastrointestinal symptoms. The difference in the average VAS was −0.01 (95% confidence interval −2.07 to 2.05). Nor did we find a difference in the outcomes measuring mental health. Conclusion Compared with placebo, adding gluten to the diet did not induce gastrointestinal symptoms or worsened mental health in adolescents recruited from a population‐based cohort. The trial registration number is NCT04639921.