Loss-of-function mutations in the cytosine-5 RNA methylase NSUN2 cause neurodevelopmental disorders in humans, yet the underlying cellular processes leading to the symptoms that include microcephaly remain unclear. Here, we show that NSUN2 is expressed in early neuroepithelial progenitors of the developing human brain, and its expression is gradually reduced during differentiation of human neuroepithelial stem (NES) cells in vitro. In the developing $Nsun2$$\mathrm{<mrow\; data-mjx-texclass="ORD">-<mrow\; data-mjx-texclass="ORD">/</mrow>-</mrow>}$ mouse cerebral cortex, intermediate progenitors accumulate and upper-layer neurons decrease. Loss of NSUN2-mediated methylation of tRNA increases their endonucleolytic cleavage by angiogenin, and 5' tRNA fragments accumulate in $Nsun2$$\mathrm{<mrow\; data-mjx-texclass="ORD">-<mrow\; data-mjx-texclass="ORD">/</mrow>-</mrow>}$ brains. Neural differentiation of NES cells is impaired by both $NSUN2$ depletion and the presence of angiogenin. Since repression of NSUN2 also inhibited neural cell migration toward the chemoattractant fibroblast growth factor 2, we conclude that the impaired differentiation capacity in the absence of NSUN2 may be driven by the inability to efficiently respond to growth factors.