Alternative splicing and polyadenylation represent two major steps in pre-mRNA processing, which ensure proper gene expression and diversification of human transcriptomes. Deregulation of these processes concurs to oncogenic programs involved in onset, progression and evolution of human cancers, which often result in acquisition of resistance to existing therapies. On the other hand, cancer cells frequently increase their transcriptional rate and develop a transcriptional addiction, which imposes a high stress on the pre-mRNA processing machinery and establishes a therapeutically exploitable vulnerability. A prominent role in fine-tuning pre-mRNA processing mechanisms is played by three main families of protein kinases: SRPK, CLK and CDK. These kinases phosphorylate the RNA polymerase, splicing factors and regulatory proteins involved in cleavage and polyadenylation of the nascent transcripts. The activity of SRPKs, CLKs and CDKs can be altered in cancer cells and their inhibition was shown to exert anticancer effects. In this review, we describe key findings that have been reported on these topics and discuss challenges and opportunities of developing therapeutic approaches targeting splicing factor kinases.