Renal cell carcinoma (RCC) is the most lethal of all urological malignancies because of its potent metastasis potential. Melatonin exerts multiple tumor‐suppressing activities through antiproliferative, proapoptotic, and anti‐angiogenic actions and has been tested in clinical trials. However, the antimetastastic effect of melatonin and its underlying mechanism in RCC are unclear. In this study, we demonstrated that melatonin at the pharmacologic concentration (0.5–2 mm) considerably reduced the migration and invasion of RCC cells (Caki‐1 and Achn). Furthermore, we found that melatonin suppressed metastasis of Caki‐1 cells in spontaneous and experimental metastasis animal models. Mechanistic investigations revealed that melatonin transcriptionally inhibited MMP‐9 by reducing p65‐ and p52‐DNA‐binding activities. Moreover, the Akt‐mediated JNK1/2 and ERK1/2 signaling pathways were involved in melatonin‐regulated MMP‐9 transactivation and cell motility. Clinical samples revealed an inverse correlation between melatonin receptor 1A (MTNR1A) and MMP‐9 expression in normal kidney and RCC tissues. In addition, a higher survival rate was found in MTNR1A^high/MMP‐9^low patients than in MTNR1A^low/MMP‐9^high patients. Overall, our results provide new insights into the role of melatonin‐induced molecular regulation in suppressing RCC metastasis and suggest that melatonin has potential therapeutic applications for metastastic RCC.