SIGNIFICANCE: Current methods for complex conjugate removal (CCR) in frequency-domain optical coherence tomography (FD-OCT) often require additional hardware components, which increase system complexity and cost. A software-based solution would provide a more efficient and cost-effective alternative. AIM: We aim to develop a deep learning approach to effectively remove complex conjugate artifacts (CCAs) from OCT scans without the need for extra hardware components. APPROACH: We introduce a deep learning method that employs generative adversarial networks to eliminate CCAs from OCT scans. Our model leverages both conventional intensity images and phase images from the OCT scans to enhance the artifact removal process. RESULTS: Our CCR-generative adversarial network models successfully converted conventional OCT scans with CCAs into artifact-free scans across various samples, including phantoms, human skin, and mouse eyes imaged CONCLUSIONS: Our method provides a low-cost, data-driven, and software-based solution to enhance FD-OCT imaging capabilities by the removal of CCAs.