Background: Cerebrospinal fluid (CSF) provides basic mechanical and immunological protection to the brain. Historically, analysis of CSF has focused on protein changes, yet recent studies of neurodegenerative diseases have shed light on cellular alterations. Due to low cell numbers in the CSF, only recently have advances in molecular biology techniques allowed for the investigation of disease-related cellular changes. Chief among these advances is single cell RNA sequencing (scRNAseq). However, concerns such as batch effects and time constraints call for a standardized method for long-term preservation of CSF immune cells. Results: We present a method for long-term cryopreservation of CSF immune cells for downstream scRNAseq analysis. Cells can be analyzed up to two years following CSF collection. On average, 4,961 live cells can be recovered from 10 mL CSF after cryopreservation, with no association between length of storage and cell viability. We demonstrate that scRNAseq detects CD8 + and CD4 + T cells, natural killer cells, plasma cells, B cells, and innate immune cells (monocytes and dendritic cells) within the CSF of 24 subjects. Conclusions: The ability to store CSF cells long-term will enable researches actively collecting CSF to investigate intrathecal immunity. This method will aid in the understanding of cellular and molecular changes to CSF immunity in neurodegenerative diseases.