The apicomplexa comprise a large phylum of single-celled, obligate intracellular protozoa that infect humans and animals and cause severe parasitic diseases. Available therapeutics against these devastating diseases are limited by suboptimal efficacy and frequent side effects, as well as the emergence and spread of resistance. Here, we use a drug repositioning strategy and identify altiratinib, a compound originally developed to treat glioblastoma, as a promising drug candidate with a broad range of activity against apicomplexans. Altiratinib is parasiticidal and blocks the development of intracellular zoites in the nanomolar range and with a high selectivity index. We identified TgPRP4K of T. gondii as the primary target of altiratinib by genetic target deconvolution, highlighting key residues within the kinase catalytic site that, when mutated, confer resistance to the drug. We have further elucidated the structural basis of the inhibitory mechanism and the species selectivity of altiratinib for TgPRP4K, as well as for its Plasmodium falciparum counterpart PfCLK3. Our data also highlight the structural features critical for binding of the other PfCLK3 inhibitor, TCDM-135051. Consistent with the role of this kinase family in splicing in a broad spectrum of eukaryotes, we have shown that altiratinib causes global disruption of splicing, primarily through intron retention in both T. gondii and P. falciparum, but not in Cryptosporidium parvum, where the kinase has been lost during evolution. Thus, our data establish parasitic PRP4K/CLK3 as a promising pan-apicomplexan target whose repertoire of inhibitors can be expanded by the addition of altiratinib.