Spliced leader (SL) trans-splicing is a key step in the processing of many mRNAs in different eukaryotic lineages, including in parasitic flatworms. Despite its importance, efforts for its characterization in this phylum have remained a collection of single-species studies with little exploration at a wider phylogenetic context. In this work, we present a comprehensive analysis of this process, based on the available genomic and transcriptomic data of 24 cestode and trematode species, including the identification of the SL-RNA sequences and their splicing acceptor transcripts and sites. We identified a main pattern of concerted evolution of SL-RNA loci in most flatworm species, as well as divergence of SL-RNA loci in selected species. However, even in species with several divergent SL-RNAs, there was no specialization in their targets. This, along with low SL trans-splicing levels, is in stark contrast with the global patterns of SL trans-splicing usage in nematodes. SL trans-splicing could be detected for a limited number of mRNAs in all species (<31%), and we found extensive use of the same splice acceptor sites for cis-splicing, especially for monocistronic transcripts. Ancestral SL trans-splicing sites are found in many conserved genes, including in putative ancestral operons that are shared between cestodes and trematodes.