As commissural axons approach and enter the midline, Netrin/DCC signaling promotes axonal outgrowth and midline attraction. Nova1/2 regulate Dcc alternative splicing by promoting the production of the full-length Dcclong isoform. In Nova1/2 dKO embryos, Dcclong is reduced and fewer axons are able to reach the midline, phenocopying Dcc KO mutants. In precrossing axons, SLIT/ROBO repulsion is repressed by multiple genes including Prrg4, miR-92, and Robo3 to allow midline entry. We show here that ROBO repulsion is not uniformly repressed precrossing, but is developmentally controlled such that ROBO repulsion is active early on to prevent premature crossing and is sufficiently inhibited later to allow crossing. This is achieved through the regulation of Robo1/2 alternative splicing at microexon 6b by the NOVA splicing factors. As NOVAs increase during development, the Robo1/2(e6b+) isoform, which has a greater repulsive activity, is reduced, whereas the Robo1/2(e6b-) isoform is upregulated. In Nova1/2 dKO embryos, e6b+ is abnormally elevated and the axons that are able to reach the midline often fail to enter. A similar and more complete defect is present in Robo3 KO embryos and partial loss of function in Robo3 and Nova1/2 synergistically blocks midline entry. Upon entering the midline, SLIT/ROBO repulsion is upregulated, which facilitates axonal exit, blocks recrossing, and guides postcrossing axons to appropriate lateral positions. Robo1(e6b-) directs the axons medially, while Robo1(e6b+) and Robo2 guide the axons dorsolaterally. Double knockout of Nova1/2 reduces the medial tract and increases the dorsolateral tract.