Provided are a method of preparing a gel polymer electrolyte secondary battery, and a gel polymer electrolyte secondary battery prepared by the method. The gel polymer electrolyte secondary battery includes a cathode, an anode, a separator and a gel polymer electrolyte in a battery case. The method includes (S1) coating a polymerization initiator on a surface of at least one selected from a group consisting of a cathode, an anode, a separator of a non-woven fabric, and a battery case, the surface needed to be contacted with a gel polymer electrolyte; (S2) putting an electrode assembly including the cathode, the anode, the separator of a non-woven fabric into the battery case; and (S3) forming a gel polymer electrolyte by introducing a gel polymer electrolyte composition including an electrolyte solvent, an electrolyte salt and a polymer electrolyte monomer into the battery case, and polymerizing the monomer.