The effects of cocoa-derived polyphenols on cognitive functions have been analyzed through numerous studies using different interventions (doses, vehicles, time frame, cognition tests, and characteristics of participants) which may hamper the interpretation and comparison of findings across investigations. Thus, a systematic review was conducted to analyze the effects of cocoa-derived polyphenols intake on human cognition and discuss the methodological aspects that may contribute to the heterogeneity of findings. Randomized clinical trials evaluating the effect of cocoa polyphenols on cognitive function in healthy subjects were selected according to selection criteria. Twelve studies were selected. Quality was assessed according to the Cochrane risk for bias tool. The most common risk for bias was the lack of information about the sequence generation process. Effects on cognitive function were observed after consumption of 50mg/day of (-)-epicatechin and in studies using a component-matched placebo and cocoa as the polyphenol vehicle given to healthy adults (18-50years). Memory (n = 5) and executive function (n = 4) showed the most significant effects with medium and large effect sizes after intake of intermediate doses of cocoa flavanols (500-750mg/day). Overall, this set of studies suggest a positive effect of cocoa polyphenols on memory and executive function. However, the available evidence is very diverse and future studies may address the identified sources of variation to strengthen current evidence on this promising field.