To generate integrated organized molecular properties, multiple molecular components are required to be assembled into the molecular system with sequential and spatial accuracy in accordance with the design of the molecular assembly. Herein, we present a novel programmable synthesis of a cofacially stacked porphyrin array via repetitive construction of a peptide duplex. We designed and synthesized a novel porphyrin having two artificial amino acid moieties at the trans meso-positions. The amino acid moieties can be connected with another porphyrin unit by repetitive doubly coupling reactions to afford the peptide duplex bridged by the porphyrins. In the duplex, the porphyrin units are stacked cofacially, and the efficient electronic communication among the arrayed porphyrin units was characterized by split redox waves in the cyclic voltammograms. We also demonstrated the three different square-planar metal ions, namely Cu(2+), Ni(2+), and Pd(2+), were arranged inside the ladder-type porphyrin array in a programmable fashion.