PURPOSE: A cell permeable fusion protein for enhancing stem cell regeneration is provided to promote stem cell differentiation and to maintain and recover stem cell functionality. CONSTITUTION: A cell permeable fusion protein for enhancing stem cell regeneration or proliferation contains cell permeable peptides conjugated at amino terminal of a protein with an antioxidative or proliferative function. The protein with antioxidative function is SOD of sequence number 1, thioredoxin of sequence number 2, or derivative thereof. The protein with proliferative function is HOX4 of sequence number 3, NF-Ya of sequence number 4, or a derivative thereof. A method for preparing the fusion proteins comprises: a step of culturing a recombinant microorganism transformed by an expression vector of the fusion protein and expressing the fusion proteins; and a step of collecting the expressed fusion proteins.본 발명은 줄기세포 재생 강화용 세포 침투성 융합 단백질에 관한 것으로, 더욱 자세하게는 줄기세포의 분화촉진능, 세포 사멸 억제능, 줄기세포의 기능성 유지 및 스트레스에 의해 억제된 줄기세포의 기능성을 회복하기 위한 줄기세포 재생 강화용 세포 침투성 융합 단백질에 관한 것이다.