MOTIVATION: Long-read sequencing has made RNA isoform detection and characterization more accessible. While several bioinformatics tools have been developed to examine the data generated by these approaches, a major challenge in the field has been comparing isoform profiles across several samples. RESULTS: We developed isoSeQL, a tool for compiling long-read transcriptomic data, identifying common and unique isoforms across multiple samples, and extracting and visualizing various metrics. isoSeQL will augment approaches that utilize long-read sequencing to discover novel isoforms and to examine how isoforms vary across different experimental and biological conditions and cell types. We demonstrate how to use isoSeQL with publicly available datasets. AVAILABILITY AND IMPLEMENTATION: isoSeQL is available on Github: https://github.com/christine-liu/isoSeQL and Zenodo:https://doi.org/10.5281/zenodo.15717809.