Liquid biopsy has obvious advantages over invasive sampling methods. Cell-free DNA is now widely used in prenatal and cancer diagnosis. Cell-free RNA is relatively unstable but could contain potential biomarkers, and some studies have demonstrated that cfRNA sequencing may be developed to be a promising diagnostic assay for disease detection. In this chapter, we introduce a modified protocol for the detection of cfRNA based on next-generation sequencing (NGS). This protocol has been specifically optimized for low-input, fragmented cfRNA samples.