Neurodegenerative diseases usually present as progressive impairment of the motor or mental functions of the central or peripheral nervous system, which is often linked to genetic and biochemical factors. The main features include synaptic and neuronal deficits, abnormal protein homeostasis, DNA and RNA defects, inflammation, and pathological protein aggregation. Clinical evidence suggests that circadian rhythms affect different neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, through oxidative stress, neuroinflammation, and other mechanisms. Disruptions in circadian rhythms, which are often linked to alterations in RNA modifications, contribute to disease progression. This review provides an overview of current research progress on neurodegenerative diseases and outlines their relationship in terms of aberrant circadian rhythm, highlights the role of RNA modifications in circadian rhythm-regulated neurodegenerative diseases, and presents the potential applications of RNA-based drugs for treating neurodegenerative diseases.