In recent years, the intricate interplay between sirtuins and melatonin has emerged as a fascinating area of research, with profound implications on various aspects of human health. This comprehensive chapter delves into the complex relationship between sirtuins and melatonin, as well as their essential roles in the regulation of circadian rhythms, inflammation, and aging. The attention is primarily directed to their impact on a range of critical health focal points, including cardiovascular diseases, central nervous system disorders, metabolic imbalances, musculoskeletal disorders, neoplasms, and the overarching process of aging, detailing all the complex biochemical mechanisms and physiological pathways that validate the intimately tailored functional relationship between the indoleamine hormone synthesized in the pinealocytes and the NAD+-dependent histone deacetylases. These two components interact in complex ways, influencing processes such as cellular homeostasis, oxidative stress, and inflammatory cascade regulation. Age-related reductions in SIRT1 expression, influenced by melatonin levels, can deeply impact cellular functions. By elucidating the complex connections between sirtuins, melatonin, and chronobiological processes, we contribute to a deeper understanding of the fundamental mechanisms that trigger inflammation and aging-related diseases, and in the meantime underscore the promising avenues for future research and clinical interventions aimed at enhancing human health and extending the quality of life.