Neuropeptide cocaine‐ and amphetamine‐regulated transcript (CART) is widely expressed in the brains of teleosts, amphibians, birds, and mammals and has emerged as a conserved regulator of energy balance across these vertebrate phyla. However, as yet, there is no information on CART in the reptilian brain. We characterized the cDNA encoding CART and mapped CART‐containing elements in the brain of gecko, Hemidactylus leschenaultii (hl) using a specific anti‐CART antiserum. We report a 683‐bp hlcart transcript containing a 336‐bp open reading frame, which encodes a putative 111‐amino acid hl‐preproCART. The 89‐amino acid hl‐proCART generated from hl‐preproCART produced two putative bioactive hl‐CART‐peptides. These bioactive CART‐peptides were > 93% similar with those in rats/humans. Although reverse transcription‐polymerase chain reaction (RT‐PCR) detected hlcart‐transcript in the brain, CART‐containing neurons/fibers were widely distributed in the telencephalon, diencephalon, mesencephalon, rhombencephalon, spinal cord, and retina. The mitral cells in olfactory bulb, neurons in the paraventricular, periventricular, arcuate (Arc), Edinger–Westphal, and brainstem nuclei were intensely CART‐positive. In view of antagonistic roles of neuropeptide Y (NPY) and CART in energy balance in the framework of mammalian hypothalamus, we probed CART–NPY interaction in the hypothalamus of H. leschenaultii. Double immunofluorescence showed a dense NPY‐innervation of Arc CART neurons. Ex vivo hypothalamic slices treated with NPY/NPY‐Y1‐receptor agonist significantly reduced hlcart‐mRNA levels in the Arc‐containing tissues and CART‐ir in the dorsal‐Arc. However, CART‐ir in ventral‐Arc was unaffected. NPY via Y1‐receptors may regulate energy balance by inhibiting dArc CART neurons. This study on CART in a reptilian brain fills the current void in literature and underscores the conserved feature of the neuropeptide across the entire vertebrate phyla.