Abstract Background Postprandial glycaemic response affects cognitive and vascular function. The acute effect of breakfast glycaemic index on vascular parameters is not sufficiently known. Also, the influence of breakfasts with different glycaemic index on cognitive performance has been mostly studied in children and adolescents with varying results. Therefore, the purpose of this study is to analyse the postprandial effect of high and low glycaemic index breakfasts on vascular function and cognitive performance and their relationship with postprandial glycaemic response in healthy young adults. Methods/design This is a crossover clinical trial targeting adults (aged 20–40 years, free from cardiovascular disease) selected by consecutive sampling at urban primary care health clinics in Salamanca (Spain). Each subject will complete three interventions with a washout period of one week: a control condition (consisting of water); a low glycaemic index breakfast (consisting of dark chocolate, walnuts, yogurt and an apple, with an overall glycaemic index of 29.4 and an energy contribution of 1489 kJ); and a high glycaemic index breakfast (consisting of bread, grape juice and strawberry jam, with an overall glycaemic index of 64.0 and an energy contribution of 1318 kJ). The postprandial effect will be assessed at 60 and 120 minutes from each breakfast including blood sampling and cognitive performance evaluations. Measurements of arterial stiffness and central haemodynamic parameters will be taken at –10, 0, 15, 30, 45, 60, 75, 90, 105 and 120 minutes. Discussion The differences in postprandial glycaemic response due to breakfast glycaemic index could affect vascular parameters and cognitive performance with important applications and implications for the general population. This could provide necessary information for the establishment of new strategies in terms of nutritional education and work performance improvement. Trial registration ClinicalTrials.gov: NCT02616276 . Registered on 19 November 2015.