The complete inventory of regulatory factors in human spliceosomes remains unknown, and many flexibly bound components are not revealed in present spliceosome structures. The intrinsically unstructured C9ORF78 protein was detected in C complex spliceosomes but is not contained in present spliceosome structures. We found a tight interaction between C9ORF78 and the key spliceosome remodeling factor, BRR2, in a large-scale yeast two-hybrid screen, validated by targeted in vitro assays. Affinity purification/mass spectrometry and RNA UV-crosslinking analyses identified several additional C9ORF78 interactors in spliceosomes. High-resolution cryogenic electron microscopy structures revealed how C9ORF78 and the spliceosomal B complex protein FBP21 wrap around the C-terminal helicase cassette of BRR2 in a mutually exclusive manner. Knock-down of C9ORF78 led to global alternative splicing changes, including a substantial usage of alternative NAGNAG 3’-splice sites, at least in part dependent on BRR2. Comparison of our structure to C* complex spliceosomes shows that C9ORF78 could contact several detected interactors from its BRR2 “home base”, in particular the RNA helicase PRPF22, a suggested 3’-splice site regulator. Together our data firmly establish C9ORF78 as a novel, late-stage splicing regulatory protein that takes advantage of a multi-factor trafficking site on BRR2, providing one explanation for the suggested, but puzzling, roles of BRR2 during splicing catalysis and alternative splicing.