Abstract Motivation Functional annotation is a common part of microRNA (miRNA)-related research, typically carried as pathway enrichment analysis of the selected miRNA targets. Here, we propose miRAnno, a fast and easy-to-use web application for miRNA annotation. Results miRAnno uses comprehensive molecular interaction network and random walks with restart to measure the association between miRNAs and individual pathways. Independent validation shows that miRAnno achieves higher signal-to-noise ratio compared to the standard enrichment analysis. Availability and implementation miRAnno is freely available at https://ophid.utoronto.ca/miRAnno/. Supplementary information Supplementary data are available at Bioinformatics online.