Background: Sperm DNA fragmentation (SDF) can affect fertilization rate and embryo development, making it a useful measure for assessing male fertility. Available evidence supports the association between high sperm DNA fragmentation and poor outcomes, with regard to natural conception. Several treatment options are being adopted with varying degrees of success. Some of the commonly used treatment options are the intake of oral antioxidants, varicocele repair, and techniques like micromanipulation-based sperm selection and use of testicular sperm for intracytoplasmic sperm injection. Case Presentation: Studies have shown that around 29% of couples depend on complementary and alternative medicine (CAM) modality for the treatment of infertility. However, there is a lack of substantial evidence regarding its efficacy in treating various aspects of infertility in couples. The current case report is about a 44 year-old male patient with infertility, who has a known diagnosis of sex chromosome abnormalities. Meanwhile, the SDF study reports indicated the presence of chromosomal abnormalities. This patient was treated exclusively with Ayurveda therapy aimed towards qualitative improvement in reproductive tissues (Shukra Dhatu as per Ayurveda). Patient was assessed periodically for changes in chromosomal abnormality. After four months of treatment, the evaluations demonstrated the presence of completely normal chromosomes. Conclusion: This case study indicates the potential of Ayurveda therapy in treating cases of male infertility caused by DNA fragmentation. Furthermore, observations and systematically designed clinical trials are warranted to establish a stronger level of evidence before making further clinical recommendations.