The aim of this paper was to explore the interplay between ketogenic dietary therapies (KDTs) and gut microbiota composition, focusing on their potential implications for rare neurological and inherited metabolic disorders (IMDs), and also autism spectrum disorder. A literature search was conducted using PubMed (Medline) for articles published between 2016 and July 2025. A total of 251 articles were screened, and 22 were included based on relevance to KDTs, microbiota, and rare neurological or metabolic diseases in pediatric and adult populations. KDTs have been reported to induce significant shifts in gut microbiota composition across rare neurological and metabolic disorders. Common findings included reduced levels of the genus Bifidobacterium and members of the Firmicutes-related genera, along with an increased abundance of Bacteroides and Akkermansia. In drug-resistant epilepsy, these changes correlated with seizure reduction; in autism spectrum disorder and mitochondrial disorders, KDTs modulated inflammatory and neuroactive microbial profiles. Microbiota was frequently modified in its composition and metabolite production, with a potential neuroprotective and metabolic effect. While ketogenic diets represent a promising therapeutic strategy across rare neurological and metabolic disorders, their interplay with the gut microbiota is complex and unclarified yet. Mechanistic and translational studies will be essential to harness microbiota-driven effects, improve personalization of therapy, and ensure long-term safety in both pediatric and adult populations.