Brown adipocytes (BAs) are specialized for adaptive thermogenesis and, upon sympathetic stimulation, activate mitochondrial uncoupling protein (UCP)‐1 and oxidize fatty acids to generate heat. The capacity for brown adipose tissue (BAT) to protect against obesity and metabolic disease is recognized, yet information about which signals activate BA, besides β3‐adrenergic receptor stimulation, is limited. Using single‐cell transcriptomics, we confirmed the presence of mRNAs encoding traditional BAT markers (i.e., UCP1, expressed in 100% of BAs Adrb3, expressed in <50% of BAs) in mouse and have shown single‐cell variability (>1000‐fold) in their expression at both the mRNA and protein levels. We further identified mRNAs encoding novel markers, orphan GPCRs, and many receptors that bind the classic neurotransmitters, neuropeptides, chemokines, cytokines, and hormones. The transcriptome variability between BAs suggests a much larger range of responsiveness of BAT than previously recognized and that not all BAs function identically. We examined the in vivo functional expression of 12 selected receptors by micro‐injecting agonists into live mouse BAT and analyzing the metabolic response. In this manner, we expanded the number of known receptors on BAs at least 25‐fold, while showing that the expression of classic BA markers is more complex and variable than previously thought.—Spaethling, J. M., Sanchez‐Alavez, M., Lee, J., Xia, F. C., Dueck, H., Wang, W., Fisher, S. A., Sul, J.‐Y., Seale, P., Kim, J., Bartfai, T., Eberwine, J. Single‐cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis. FASEB J. 30, 81‐92 (2016). www.fasebj.org