Chocolate has a history of human consumption tracing back to 400 AD and is rich in polyphenols such as catechins, anthocyanidins, and pro anthocyanidins. As chocolate and cocoa product consumption, along with interest in them as functional foods, increases worldwide, there is a need to systematically and critically appraise the available clinical evidence on their health effects. A systematic search was conducted on electronic databases such as MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials (CENTRAL) using a search strategy and keywords. Among the many health effects assessed on several outcomes (including skin, cardiovascular, anthropometric, cognitive, and quality of life), we found that compared to controls, chocolate or cocoa product consumption significantly improved lipid profiles (triglycerides), while the effects of chocolate on all other outcome parameters were not significantly different. In conclusion, low-to-moderate-quality evidence with short duration of research (majority 4–6 weeks) showed no significant difference between the effects of chocolate and control groups on parameters related to skin, blood pressure, lipid profile, cognitive function, anthropometry, blood glucose, and quality of life regardless of form, dose, and duration among healthy individuals. It was generally well accepted by study subjects, with gastrointestinal disturbances and unpalatability being the most reported concerns.