Anodized aluminum oxide (AAO) nanochannels of diameter, D, of ~50 nm and length, L, of ~60 µm (L/D: approx. 1200 in the aspect ratio), were synthesized and applied as an electrode for the electrochemical growth of Co/Cu multilayered heterojunction nanocylinders. We synthesized numerous Co/Cu multilayered nanocylinders by applying a rectangular pulsed potential deposition method. The Co layer thickness, tCo, ranged from ~8 to 27 nm, and it strongly depended on the pulsed-potential condition for Co layers, ECo. The Cu layer thickness, tCu, was kept at less than 4 nm regardless of ECo. We applied an electrochemical in situ contact technique to connect a Co/Cu multilayered nanocylinder with a sputter-deposited Au thin layer. Current perpendicular-to-plane giant magnetoresistance (CPP-GMR) effect reached up to ~23% in a Co/Cu multilayered nanocylinder with ~4760 Co/Cu bilayers (tCu: 4 nm and tCo: 8.6 nm). With a decrease in tCo, (ΔR/Rp)−1 was linearly reduced based on the Valet–Fert equation under the condition of tF > lFsf and tN < lNsf. The cobalt spin-diffusion length, lCosf, was estimated to be ~12.5 nm.