Melatonin (MLT) is a natural indolic hormone and its antioxidant activity has been reported through various mechanisms. MLT interacts with the estrogen signaling pathway by inhibiting aromatase enzyme, and it has been suggested that these new compounds may have endocrine‐related adverse effects due to their selective estrogen modulator activity. In this study, we investigated the aromatase inhibitory and estrogen receptor agonist/antagonist effects as well as possible antioxidant activity of MLT analogue 5‐floro indole derivatives for being potential drug candidates in the prevention and treatment of oxidative stress related diseases. Among the 34 compounds tested, three compounds showed antioxidant effect through radical scavenging activity and reducing the formation of intracellular reactive oxygen species. They also showed varying potencies of antiestrogenic and/or aromatase inhibitory activity which should be considered as a potential untargeted effect of MLT and its analogues.