Convergent extension (CE) is the narrowing and lengthening of an embryonic field along a defined axis. It underlies a variety of complex morphogenetic movements, such as mesoderm elongation and neural tube closure in vertebrate embryos. Convergent extension relies on the same intracellular molecular machinery that directs planar cell polarity (PCP) in epithelial tissues, including non-canonical Wnt signaling components. However, it is not known what signals coordinate CE movements across cell fields. In the simple chordate Ciona intestinalis, the notochord plate consists of just 40 cells, which undergo mediolateral convergence (intercalation) to form a single cell row. Here we present evidence that a localized source of FGF3 in the developing nerve cord directs notochord intercalation through non-MAPK signaling. A dominant-negative form of the Ciona FGF receptor suppresses the formation of polarized actin-rich protrusions in notochord cells, resulting in defective notochord intercalation. Inhibition of Ciona FGF3 activity results in similar defects, even though it is expressed in an adjacent tissue: the floor plate of the nerve cord. In Xenopus mesoderm explants, inhibiting FGF signaling perturbs CE and disrupts membrane localization of Dishevelled (Dsh), a key regulator of PCP and CE. We propose that FGF signaling coordinates CE movements by regulating PCP pathway components such as Dsh.