Ectolecithality is a form of oogenesis unique within Metazoa but common in Platyhelminthes, in which nearly-yolkless oocytes and tightly associated yolk cells are deposited together in egg capsules. Despite profound impacts on the embryogenesis and morphology of its beneficiaries, the origins of this developmental phenomenon remain obscure. Traditionally, all ectolecithal flatworms were grouped in a clade called Neoophora. However, there are also morphological arguments for multiple origins of ectolecithality, and Neoophora has to date seen little support from molecular phylogenetic research, largely due to gaps in taxon sampling. Accordingly, we present a molecular phylogeny focused on resolving the deepest divergences among the free-living Platyhelminthes. Species were chosen to completely span the diversity of all major endo- and ectolecithal clades, including several aberrant species of uncertain systematic affinity, and additionally a thorough sampling of the “lecithoepitheliate” higher taxa Prorhynchida and Gnosonesimida, respectively under- and unrepresented in phylogenies to date. Our analyses validate the monophyly of all classical higher platyhelminth taxa, and also resolve a clade possessing distinct yolk-cell and oocyte generating organs (which we name Euneoophora new taxon). Furthermore, implied-weights parsimony and Bayesian mixture model analyses suggest common ancestry of this clade with the lecithoepitheliates, implying that these taxa may retain a primitive form of ectolecithality. This topology thus corroborates the classical hypothesis of homology between yolk cells and oocytes in all Neoophora, and should serve to guide future evolutionary research on this unique developmental innovation in Platyhelminthes.