In the present work we investigate the influence of deposition sequences on the two layers forming a CuO/Zinc oxide (ZnO) heterojunction. Both layers are prepared using the simple and cost-effective technique of spray pyrolysis. The advantage of this technique is the ability to deposit both layers successively without interruption. For this purpose, four devices are prepared by successfully changing the deposition order of ZnO and CuO layers, and after a delay for the cooling of the first deposited layer. The I–V characteristics of the realized devices reveal that the deposition order plays a crucial role in the device’s performance. We inferred that the deposition of ZnO as the first layer followed by the immediate CuO leads to a device with superior quality, i.e., low ideality factor, low reverse current, and high rectifying ratio. The SEM image and EDX analysis at the interfaces revealed the diffusion of Zn in the CuO layer, while no diffusion of Cu in the ZnO layer was observed. Estimating the density of the interface states from the conductance vs. frequency measurements (G–f) indicates that the direct deposition of CuO on ZnO leads to a lower interface density of states.