RNA binding proteins (RBPs) are major post-transcriptional regulators (PTR). In higher eukaryotes, RBPs control transcription, RNA transport, splicing and degradation, translation and translational repression and play key roles in cell fating, pluripotency and differentiation. Surprisingly, the eukaryotic RBPome is fundamentally unchanged from yeast to humans. This suggests many novel RBPs emerged in basal eukaryotes. Yet this is largely unstudied. Our phylogenomic RBPs atlas across the tree of life reveals that the eukaryotic RBPome is shaped by bacterial and archaeal RBP systems, alongside the emergence and expansion of “novel RBP” families. We characterised the RBPome of Giardia duodenalis, an early-branching single-celled eukaryote predating yeast by a billion years, uncovering the origins of key "eukaryotic innovative" RBPs. These RBPs mediate RNA splicing, silencing, translational repression, and cellular fate regulation, demonstrating the ancient emergence of critical eukaryotic PTR innovations. Comprehensive characterisation of the Giardia duodenalis RBPome, integrating in silico modelling, transcriptomics, proteomics, and interactome capture, revealed a diverse repertoire of canonical and non-canonical (moonlighting) RBPs. Functional genetics, RNA-network capture, phase-separation assays of key RBPs, including early Pumilio homologs (PUF, PUM) and helicases DDX3x and EIF4A, and “moonlighting RBPs” (Phosphoglycerate Kinase) suggests Giardia RBPs exhibit complexity and sophistication comparable to higher eukaryotes, with roles in translational repression, biological condensates, and cell differentiation. Our findings suggest that complex RBP regulation emerged early in eukaryotic evolution, potentially pivotal for eukaryotic emergence and evolution.