Painful neuroma formation is a common and debilitating sequela of traumatic or oncologic nerve amputations. Studies suggest that isolating transected nerve stumps within protective caps during amputation surgery or revision procedures may assist in preventing symptomatic nerve-end neuroma formation. This study evaluated the local effects of two porcine small intestine submucosa (pSIS) nerve caps of differing configurations on a terminal nerve end in an animal model. The tibial nerves of 57 Sprague Dawley rats were transected and transposed to the lateral hind leg. The nerves were treated with one of three SIS materials, including (i) a nerve cap with spiraling chambering, termed spiral nerve cap (SNC), (ii) a nerve cap with bifurcated chambers termed chambered nerve cap (CNC), or (iii) an open tube. The surgical control consisted of nerve stumps that were not treated. Overall tissue response, axonal swirling, optical density of axons, and behavioral pain response were quantified at 8 and 12 weeks postoperatively. There were no notable differences between the performance of the SNC and CNC groups. The pSIS nerve caps mitigated aberrant axonal regeneration and decreased neuroma formation and associated pain response. These findings suggest that nerve caps with internal chambers for axonal outgrowth may improve axonal alignment, therefore reducing the likelihood of symptomatic neuroma formation.