Extracellular RNAs (exRNA) are gaining considerable interest for their potential use as biomarkers and their role in intercellular communication. Small RNA-sequencing has been widely adopted to shed light on the diversity of exRNA in biofluids, but the field faces unique technical challenges. In particular, exRNA samples are more vulnerable to contamination and artifacts from different isolation techniques, are present in lower concentrations than cellular RNA, and are occasionally of exogenous origin. To address these challenges we present the extracellular RNA processing toolkit (exceRpt), the standardized small RNA-seq analysis pipeline of the NIH Extracellular RNA Communication Consortium (ERCC) optimized for exRNA analysis. exceRpt is structured as a cascade of filters and quantifications prioritized based on the confidence of a given set of annotated RNA. The pipeline generates quality control reports and abundance estimates for RNA biotypes, and is also capable of characterizing mappings to exogenous genomes, which can be used to generate phylogenetic trees. exceRpt has uniformly processed all (currently ~2500) exRNA-seq datasets in the public exRNA atlas.