Melatonin is known as a regulator of circadian sleep and waking rhythm. This hormone secreted by the pineal gland also has protective, oncostatic, and antioxidant properties. This systematic review was designed to answer the question “Is there a relationship between salivary melatonin changes and oncological diseases?”. Following the inclusion and exclusion criteria, ten studies were included, according to PRISMA statement guidelines. In all included studies, the diagnostic material was unstimulated whole saliva, in which the melatonin changes were determined by different laboratory methods. Most studies concerned changes in melatonin levels in patients with brain tumours due to a direct effect on the circadian rhythm centres. Other studies focused on disorders of melatonin secretion and its inclusion as a diagnostic marker in patients with prostate cancer and oral squamous cell carcinoma. The association between melatonin changes and sleep quality and chronotype in patients with newly diagnosed lung cancer and lymphoma survivors was also investigated. In conclusion, our systematic review may suggest trends for melatonin secretion alterations in oncological patients. However, due to the significant heterogeneity of the included reports, it is not possible to clearly determine a link between changes in salivary melatonin levels and the oncological diagnosis.