Small intestinal submucosa (SIS) has the potential for use as a natural scaffold material because of the presence of type-I and -III collagen and various cytokines. However, although the presence of growth factors in SIS leads to superior initial cell attachment and proliferation compared to synthetic polymeric scaffolds, the lack of reliable and reproducible shape controllability is a drawback. To overcome this problem, SIS was electrospun with a biodegradable and biocompatible polymer, polycaprolactone (PCL). PCL/SIS fibrous webs were fabricated with an electrospinning process using an auxiliary conical electrode to create stable micro/nanofibrous scaffolds. The hydrophilicity, mechanical properties and cellular behavior of the PCL/SIS fibrous scaffold were analyzed. In addition, aligned PCL/SIS fibrous webs were fabricated using various collector rotation speeds. As the alignment of micro/nanofibers increased, the hydrophilicity, orthotropic mechanical properties, and cellular behavior of PC-12 cells improved. These results show the potential for using PCL/SIS fibrous scaffolds as a good natural biomaterial.