Sleep disorders are becoming increasingly common, and their distinct effects on physical and mental health require elaborate investigation. Gut dysbiosis (GD) has been reported in sleep‐related disorders, but sleep apnoea is of particular significance because of its higher prevalence and chronicity. Cumulative evidence has suggested a link between sleep apnoea and GD. This Review highlights the gut–brain communication axis that is mediated via commensal microbes and various microbiota‐derived metabolites [such as short‐chain fatty acids (SCFAs), lipopolysaccharide (LPS) and trimethyl amine N‐oxide (TMAO)], neurotransmitters (such as γ‐aminobutyric acid, serotonin, glutamate, and dopamine), immune cells and inflammatory mediators, as well as the vagus nerve and hypothalamic–pituitary–adrenal (HPA) axis. This Review also discusses the pathological role underpinning GD and altered gut bacterial populations in sleep apnoea and its related comorbid conditions, particularly cognitive dysfunction. The Review also examines the preclinical and clinical evidence, which suggests that prebiotics and probiotics may potentially be beneficial in sleep apnoea and its comorbidities through restoration of eubiosis or gut microbial homeostasis that regulates neural, metabolic, and immune responses, as well as physiological barrier integrity via the gut–brain axis.