Spinal cord injury (SCI) is a complicated neuropathological condition that results in functional dysfunction and paralysis. Various treatments have been proposed including drugs, biological factors and cells administered in several ways. Stem cell therapy offers a potentially revolutionary mode to repair the damaged spinal cord after injury. Initially, stem cells were considered promising for replacing cells and tissue lost after SCI. Many studies looked at their differentiation to replace neuronal and glial cells for a better functional outcome. However, it is becoming clear that different functional improvements recognized to stem cells are due to biomolecular activities by the transplanted stem cells rather than cell replacement. This review aimed to discuss the paracrine mechanisms for tissue repair and regeneration after stem cell transplantation in SCI. It focuses on stem cell factor production, effect in tissue restoration, and novel delivery strategies to use them for SCI therapy.