MicroRNAs are short non-coding molecules which regulate translation in a gene-specific manner. MicroRNA isoforms that differ by few extra or missing nucleotides at the 5'-terminus (5'-isomiR) show strikingly different target specificity. This study aimed to identify functional roles of 5′-isomiR in colorectal cancers. Transcriptomic targets of microRNA isoforms were predicted using bioinformatics tools miRDB and TargetScan. The sets of putative targets identified for 5′-isomiR were integrated with mRNA and microRNA sequencing data for primary colorectal tumors retrieved from The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) database. The network of interactions among miRNA, their targets and transcription factors was built using the miRGTF-net algorithm. The results indicate that microRNA isoforms highly expressed in colorectal cancer and differing by a single nucleotide position at the 5'-terminus have ≤ 30% common targets. The regulatory network of interactions enables identification of the most engaged microRNA isoforms. Anti-correlated expression levels of canonical microRNA hsa-miR-148a-3p and its putative targets including CSF1, ETS1, FLT1, ITGA5, MEIS1, MITF and RUNX2 proliferation regulators suggest an anti-tumor role for this molecule. The canonical microRNA hsa-miR-203a-3p|0 and its 5′-isoform bind different sets of anti-correlated putative targets, although both of them interact with genes involved in the epithelial-mesenchymal transition: SNAI2 and TNC.