Developmentally regulated programmed cell death (PCD) is one of the key cellular events for precise controlling of neuronal population during postembryonic development of the central nervous system. Previously we have shown that a group of corazonin-producing peptidergic neurons (vCrz) undergo apoptosis in response to ecdysone signaling via ecdysone receptor (EcR)-B isoforms and Ultraspiracle during early phase of metamorphosis. Further utilizing genetic, transgenic, and mosaic analyses, we have found that TGF-β signaling mediated by a glia-produced ligand, Myoglianin, type-I receptor Baboon (particularly Babo-A isoform) and dSmad2, is also required autonomously for PCD of the vCrz neurons. Our studies show that TGF-β signaling is not acting epistatically to EcR or vice versa. We also show that ectopic expression of a constitutively active phosphomimetic form of dSmad2 (dSmad2PM) is capable of inducing premature death of vCrz neurons in larva but not other larval neurons. Intriguingly, the dSmad2PM-mediated killing is completely suppressed by coexpression of a dominant-negative form of EcR (EcRDN), suggesting that EcR function is required for the proapoptotic dSmad2PM function. Based on these data, we suggest that TGF-β and ecdysone signaling pathways act cooperatively to induce vCrz neuronal PCD. We propose that this type of two-factor authentication is a key developmental strategy to ensure the timely PCD of specific larval neurons during metamorphosis.