In this work, the influences of zinc oxide nanorods (ZnO NRs) arrangement, as the electron transport layer (ETL), on the photovoltaic performance of the inverted structure polymer solar cells (PSCs) were studied. Two arrangements of ZnO NRs were electrochemically synthesized on the indium tin oxide (ITO) electrode by chronoamperometry (CA) and chronopotentiometry (CP) techniques at 80 °C. Structural, morphological, optical, and electrochemical features of the prepared samples were compared using different techniques. Applying the CA technique resulted in the vertical growth of ZnO NRs on the ITO electrode. However, flower-like ZnO NRs were formed in the sample prepared by the CP method. The energy levels, charge transfer resistance, recombination resistance, and charge mobility of the prepared samples were evaluated using cyclic voltammetry and electrochemical impedance spectroscopy. Results revealed that the flower-like ZnO NRs prepared by the CP method enjoy a considerably higher (128%) charge mobility of 31.67 × 10−4 cm2/V, lower (17.6%) charge resistance of 32.82 Ω, and higher optical transparency of ∼75.52% at 550 nm. The PSC prepared based on the flower-like ZnO NRs provided a PCE of 4.45, which was about 230.57%, 145.42%, and 302.72% higher than that achieved for the ZnO nanoparticles-, and the vertical ZnO NRs-based devices, and the reference device containing no ETL. Moreover, the flower-like ZnO NRs-based PSC exhibited greater stability in the air and retained about 72% of its initial PCE after 450 h.