Emerging research highlights the pivotal role of the gut microbiota in modulating brain development and neurological function via the gut–brain axis. This chapter explores the alterations in gut microbiota among children with cerebral palsy (CP) and epilepsy, two prevalent pediatric neurological disorders often associated with gastrointestinal dysfunction and systemic inflammation. The gut–brain axis, a bidirectional communication network involving neural, immune, endocrine, and microbial pathways, has been increasingly implicated in the pathogenesis of these conditions. Dysbiosis in early life may contribute to neuroinflammation, impaired neurotransmitter production, and reduced gut barrier integrity, exacerbating neurological symptoms. We review current knowledge of normal gut microbiota development in healthy children, including key stages of colonization and factors influencing microbial composition, such as diet, birth mode, and antibiotic exposure. The impact of epilepsy and CP on microbial diversity is discussed, along with the influence of antiepileptic medications. Mechanistic pathways, such as microbial modulation of gamma-aminobutyric acid (GABA), serotonin, and short-chain fatty acids (SCFAs), are examined for their role in seizure threshold and brain function. Therapeutic interventions, including probiotics, prebiotics, the ketogenic diet, and fecal microbiota transplantation, are assessed for their potential to modulate the microbiome and improve neurological outcomes. Finally, we outline the need for multi-omics research, personalized microbiome therapies, and longitudinal clinical studies to advance pediatric neurocare. Integrating microbiome science into clinical practice offers a promising frontier for managing CP and epilepsy through targeted, microbiota-based strategies.