Background: The exact molecular mechanisms underlying sepsis remain unclear. Accumulating evidence has shown that noncoding RNAs (ncRNAs) are involved in sepsis and sepsis-associated organ dysfunction (SAOD). Methods: We performed this updated systematic review focusing mainly on research conducted in the last 5 years regarding ncRNAs associated with sepsis and SAOD. The following medical subject headings were used in the PubMed database from October 1, 2016, to March 31, 2022: “microRNA,” “long noncoding RNA,” “circular RNA,” “sepsis,” and/or “septic shock.” Studies investigating the role of ncRNAs in the pathogenesis of sepsis and as biomarkers or therapeutic targets in the disease were included. Data were extracted in terms of the role of ncRNAs in the pathogenesis of sepsis and their applicability for use as biomarkers or therapeutic targets in sepsis. The quality of the studies was assessed using a modified guideline from the Systematic Review Center for Laboratory Animal Experimentation. Results: A total of 537 original studies investigated the potential roles of ncRNAs in sepsis and SAOD. Experimental studies in the last 5 years confirmed that long ncRNAs have important regulatory roles in sepsis and SAOD. However, studies on circular RNAs and sepsis remain limited, and more studies should be conducted to elucidate this relationship. Among the included studies, the Systematic Review Center for Laboratory Animal Experimentation scores ranged from 3 to 7 (an average score of 3.78). Notably, 94 ncRNAs were evaluated as potential biomarkers for sepsis, and selective reporting of the sensitivity, specificity, and receiver operating characteristic curve was common. A total of 117 studies demonstrated the use of ncRNAs as potential therapeutic targets in sepsis and SAOD. At a molecular level, inflammation-related pathways, mitochondrial dysfunction, cell apoptosis, and/or oxidative stress were the most extensively studied. Conclusion: This review suggests that ncRNAs could be good biomarkers and therapeutic candidates for sepsis and SAOD. Prospective, large-scale, and multicenter cohort studies should be performed to evaluate specific ncRNAs as biomarkers and test the organ-specific delivery of these regulatory molecules when used as therapeutic targets.