High throughput RNA sequencing has revolutionized how we think about the regulation of gene expression by revealing enormous diversity in mRNA transcript expression across cell types and tissues. Over 90% of human genes are regulated by splicing yet changes in mRNA diversity largely remains a hidden layer of cell regulation in health and disease. We are interested in this concept in melanoma because a high degree of splicing predicts poor survival in melanoma patients, and aberrantly spliced BRAF confers resistance to BRAF and MAPK targeted therapies. However, much less is known about how global changes in splicing affects the response to anti-cancer therapies, particularly in drug tolerant cell states that emerge in the transition from responsive to resistant disease. By assessing mRNA processing events in both experimental models and patient samples on-therapy, we identified large-scale changes in exon skipping, indicative of isoform switching that we predict facilitates therapy-induced adaptation and subsequent resistance. Consistent with this idea, pathway analysis revealed enrichment of cellular processes required for drug tolerance. One of the most significant alternative splicing events identified in patients on-therapy was exon inclusion in the RNA processing factor RBM39. Importantly, we demonstrate this can produce multiple distinct protein isoforms, with distinct sub-cellular localisations and RNA processing functions. Excitingly, a clinically relevant RBM39 inhibitor synergized with MAPK targeted therapies in a panel of melanoma cell lines, reversed biomarkers of drug tolerance, and significantly delayed resistance to improve overall survival in multiple in vivo models. Mechanistically, transcriptomic analysis of combination treated cells revealed autoregulation of RBM39 splicing, whereby RBM39 mediates exon inclusion within its own mRNA. Importantly, we demonstrate this is SF3B1-dependent and SF3B1 inhibition also blocks drug tolerance induced by MAPK targeted therapies. Together, our data support a model whereby RBM39-SF3B1 dependent mRNA processing is hijacked by melanoma cells to rapidly produce new proteins required for adaptation and survival in response to MAPK therapy, and we predict this can be leveraged therapeutically to prevent resistance. To explore this further, we have now applied Nanopore long read sequencing approaches to comprehensively profile differential transcript usage during distinct phases of treatment in vivo. This approach identified thousands of novel transcripts, and hundreds of significant isoform-switching events, in melanoma tumours treated with targeted therapy. These analyses provide new insights into the post-transcriptional landscape of therapy-induced plasticity and acquired resistance in melanoma and provide potential new targets for both small molecule and mRNA-based therapies.