A midline in the developing central nervous system (CNS) is essential for the symmetric distribution of neural progenitors that later establish functional, bilaterally symmetric neural circuits. In the zebrafish hindbrain, a midline forms early during neurulation and requires a coordinated interplay of cell convergence and midline-crossing cell divisions (C-divisions). These two processes are controlled by the Wnt/planar cell polarity (PCP) pathway. However, upstream cues that control the timely production of PCP components remain unknown. Midkine (Mdk) and pleiotrophin (Ptn) are structurally related heparin-binding growth factors that are dynamically expressed in the developing zebrafish hindbrain. We used proximity ligation assays (PLAs) and fluorescence cross correlation spectroscopy (FCCS)in vivoto show that two zebrafish Mdks, Mdka and Mdkb, as well as Ptn interact with protein tyrosine phosphatase receptors type Z1, Ptprz1a and Ptprz1b, with distinct affinities. Ligand binding triggered Ptprz1b internalization and thereby determined the availability of signaling receptor on cell membranes. In zebrafishmdka, ptnandptprz1bmutants, cell migration and convergence were significantly impaired during hindbrain neurulation. Impaired convergence led to misplaced C-divisions, defective cell polarity and consequently duplicated midlines. These duplications were rescued by overexpression ofDrosophilaPrickle, a key component of the Wnt/PCP pathway. Here, we provide evidence that zygotic Mdka controls the distribution of maternally provided Ptprz1b, which in turn is needed for transcription of zebrafishprickle1b. Our findings thus reveal a role for Mdka and Ptprz1b upstream of Wnt/PCP to coordinate neural plate convergence, neural progenitor positioning and midline formation.