Injectable hydrogels for cell delivery and tissue regeneration have several advantages over pre-fabricated scaffolds that require more invasive transplantation procedures, but lack the ability to implement tunable topologies. Here, we describe an approach to create patternable and injectable scaffolds using magnetically-responsive (MR) self-assembling peptide hydrogels, and validate their efficacy to promote and align axon infiltration at the site of a spinal cord injury. In vitro experiments reveal the parameters needed to align the fibers using the application of an external magnetic field. These results indicate that applying a 100-Gauss (G) field to the peptide hydrogels during polymerization causes fiber alignment as measured by electron microscopy, even in the presence of cells. In order to mimic infiltrating axons, neural progenitor cells (NPCs) are seeded on the surface of peptide hydrogels to interrogate the effects of both magnetic alignment and embedding human mesenchymal stem cells (hMSCs) in the scaffold. NPCs infiltrate peptide hydrogels seeded with hMSCs, and exhibit increased alignment and elongation in aligned gels. In order to evaluate these injectable and patternable scaffolds in vivo, hMSC-seeded peptide hydrogels are injected at the site of a contusion spinal cord injury with and without the presence of a magnetic field to align the resulting fibrous network. Measurements of axon growth and orientation as well as inflammation and glial scar formation indicate that these metrics are improved in magnetically aligned hMSC-seeded hydrogels. The results verify that MR hydrogels can dictate the orientation of infiltrating axons, providing a viable means to control the topology of injectable scaffolds.