Uncoupling protein 1 (UCP1) catalyzes mitochondrial proton leak in brown adipose tissue to facilitate nutrient oxidation for heat production, and its activation may counteract obesity and metabolic disease in humans. The protein is activated by free fatty acids, which are generated in brown adipocytes following adrenergic stimulation (e.g. in response to cold exposure) to induce proton leak by UCP1 through an unclear interaction. Here, we have characterized activator binding to purified UCP1 by protein thermostability shift analysis, which, unlike many conventional approaches, can inform on the binding of hydrophobic ligands to membrane proteins. We show that fatty acids and other activators influence UCP1 through a specific destabilizing interaction, which can be distinguished from general denaturation induced by these ionic detergent-like species in tests. The degree of destabilization correlates with activator potency, as confirmed in liposome activity assays, and matches UCP1 destabilization induced by equivalent alkyl sulfonates that are transported by the protein, consistent with activators interacting as transport substrates that shift the carrier to a less stable conformation of the transport cycle. Through the detection of stability shifts in screens, we identify novel activators, including the over-the-counter drug ibuprofen, where ligand analysis indicates a relatively wide structural specificity for interacting molecules. Ibuprofen induces UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1-expressing HEK293 cells, but not in cultured brown adipocytes, suggesting that the targeting of UCP1 in cells by approved drugs is in principle achievable as a therapeutic avenue, but requires variants with more effective delivery in brown adipocytes.