Autoimmune diseases are characterized by the dysregulation of B-cells, which are responsible for antibody production against pathogens, and T-cells, which play a crucial role in cell-mediated immunity, including both helper and cytotoxic T-cells. These disorders frequently present with abnormal responses from both B- and T-cells, which can have a significant impact on cardiovascular health, particularly among the female patients. Key mechanisms contributing to these diseases include the activation of the NLRP3 inflammasome impaired efferocytosis is the process by which phagocytes clear apoptotic cells to maintain immune and developmental balance. Defects in this process can lead to inflammatory and autoimmune disorders. The gut microbiota helps defend against pathogens and signals immune cells, playing a vital role in human health and is involved in many aspects of the body. Novel therapeutic strategies such as nanomedicine and targeted treatments are being developed to restore immune balance. The significance of thymic homeostasis the influence of viral infections and the presence of tertiary lymphoid structures highlight the need for multidisciplinary approaches in the management of these conditions. A case study of a 9-year-old girl diagnosed with seronegative autoimmune encephalitis, who displayed severe obsessive-compulsive disorder (OCD) and aggressive behavior, exemplifies the complexities involved in treatment. Promising interventions, including CAR-T-cell therapy and nanomedicine, are under development for various autoimmune diseases, such as vitiligo and refractory autoimmune rheumatic diseases (ARDs). Furthermore, emerging therapies, including CAR-T-cell therapy, mRNA-based strategies, and microbiome modulation, are being explored alongside advancements in personalized medicine and early diagnostic techniques to improve patient outcomes for individuals affected by autoimmune diseases.