Targeted gene therapy needs to be implemented for future therapies to ensure efficient activity at the site of patient primary tumors or metastases without causing intolerable side-effects. One of the elements of gene therapy is vector, which includes viral and non-viral vector. In the present study, we constructed a novel non-viral targeted gene therapeutic system by using the new minicircle (MC) producing plasmid for Epstein-Barr virus (EBV)-positive nasopharyngeal carcinoma (NPC). Molecular cloning technique was used to construct plasmids and electrophoretic analysis. Dual-luciferase reporter assay was used to evaluate the expression of luciferase. Fluorescence microscope was used to detect the expression of enhanced green fluorescence protein (EGFP). We constructed a new MC producing system pMC.BESPX-origin of plasmid replication (oriP), and demonstrated that this system could produce highly purified MC-oriP. Furthermore, our results showed that MC-oriP vector produced by the new system could mediate targeted luciferase gene expression in EBV-positive NPC cells. In addition, we verified that MC could mediate enhanced transgene expression compared with parent plasmid through EGFP transfection. The present study constructed a targeted expression vector pMC.BESPX-oriP which could carry diversified therapeutic genes for EBV-positive NPC and provides a new approach for MC-based therapies.