High throughput RNA sequencing has revealed enormous diversity in mRNA transcript expression whereby alternative splicing produces multiple mRNAs from a single gene. Most human genes are regulated by splicing, yet mRNA diversity largely remains an understudied layer of cell regulation in health and disease. In melanoma, the extent of splicing is prognostic in patients whilst aberrantly spliced BRAF confers resistance to MAPK targeted therapies. To explore this further, we have applied both short- and long-read RNA sequencing approaches to experimental models and patient samples after treatment with MAPK targeted therapies. Analysis of short-read data from patients on-therapy identified thousands of exon-skipping events and pathway analysis identified cellular processes required for therapy-induced plasticity and resistance. One of the most significant splicing events was exon inclusion in the RNA processing factor RBM39, and we demonstrate this produces multiple protein isoforms with distinct sub-cellular localizations and functions. Notably, a clinically relevant RBM39 inhibitor synergized with MAPK targeted therapies, reversed biomarkers of drug tolerance and plasticity, and overcame resistance to improve survival in multiple in vivo models. Moreover, Cas13-mediated depletion of the alternative mRNA isoform phenocopied RBM39 protein inhibition thus demonstrating that RBM39 isoform-switching underpins its role in adaptive resistance in melanoma. To overcome limitations of short-read sequencing that lacks resolution of long-range exon connectivity, we have now comprehensively profiled the mRNA isoform repertoire in melanoma using Nanopore long-read sequencing. We identified thousands of significant isoform-switching events in melanoma tumours during distinct phases of the adaptive response to targeted therapy, including the identification of thousands of novel transcripts. These analyses provide new insights into the post-transcriptional landscape of melanoma and reveal new biology underpinning therapy-induced plasticity and acquired resistance. Collectively, we expect these approaches will provide new targets for small molecule and mRNA-based therapies to improve outcomes for melanoma patients.