Abstract Senataxin (SETX) is an RNA:DNA helicase that plays an important role in the resolution of RNA:DNA hybrids (R-loops) formed during transcription. R-loops are involved in the regulation of biological processes such as immunoglobulin class switching, gene expression, and DNA repair. Excessive accumulation of R-loops results in DNA damage and loss of genomic integrity. SETX is critical for maintaining optimal levels of R-loops to prevent DNA damage and acts as a genome guardian. Within the nucleus, SETX interacts with various RNA processing factors, and DNA damage response and repair proteins. SETX interactors include survival motor neuron (SMN) and zinc finger protein 1 (ZPR1), with whom it colocalizes in sub-nuclear bodies. Despite its ubiquitous expression, mutations in SETX specifically affect neurons and result in distinct neurodegenerative diseases such as amyotrophic lateral sclerosis type 4 (ALS4) and ataxia with oculomotor apraxia type 2 (AOA2), which are attributed to the gain-of-function and the loss-of-function mutations in SETX, respectively. In addition, low levels of SETX (loss-of-function) in spinal muscular atrophy (SMA) result in the accumulation of R-loops causing DNA damage and motor neuron degeneration. SETX may play multiple functions in diverse cellular processes, however, its emerging role in R-loop resolution and maintenance of genomic integrity is gaining attention in the field of neurodegenerative diseases. In this review, we highlight the role of SETX in R-loop resolution and its potential as a therapeutic target to treat neurodegenerative diseases.