The consumption of ultra-processed foods has increased dramatically in recent years, resulting in an overconsumption of foods that are nutritionally only suitable to be consumed occasionally. Prolonged and short-term dietary modifications can affect the composition and diversity of the gut microbiota and in turn, dysregulation of the gut microbiota may be associated with diseases of the brain. This systematic review study aimed to determine the relationship between diets high in ultra-processed foods, gut microbiota dysregulation and how this may influence early development of brain diseases. The authors first reviewed literature surrounding the role of gut microbiota on health owing to their ability to produce signalling molecules that have various functions around the body. An imbalance in the gut microbiota can result in an overproduction of signalling molecules that contribute to an unhealthy state. These signalling molecules can also act on the brain through several ways such as the nervous, circulatory, and immune systems. The review demonstrates that high fat, high sugar diets are related to increased risk for diseases such as Alzheimer’s disease and that diets high in fibre, are related to a low incidence of brain disorders, but as very few studies have looked at this in relation to gut microbiota relationships are only speculative. It was concluded that gut microbiota dysregulation could act as a clinical indicator between brain diseases and ultra-processed foods, however further studies are needed on the relationship between diet, gut microbiota and brain diseases.