A method of making an implantable neuroendoprosthetic system for transubstantiation of defects of brain, spinal cord and vegetative nervous system in a mammal in reconstructive neurosurgical operations provides a heterogeneous collagen-containing matrix for implantation, a cell preparation of autologous cells of a patient, and the cell preparation is perfused into said matrix to make an elastic cell-biopolymer biologically active mass. The cell preparation comprises placed in a NaCl solution at least one type of cells from a group comprising neural stem cells (NSC), neuroglial ensheathing cells (NGEC), endothelial cells with CD34+ marker (EC), and purified mononuclears (MN). The mass can be additionally subjected to electromagnetic radiation at 1-10 GHz before implanting.