Maturation and fine-tuning of neural circuits frequently requires neuromodulatory signals that set the excitability threshold, neuronal connectivity and synaptic strength. Here we present a mechanistic study of how neuromodulation stimulated intracellular Ca2+ signals, through the store-operated Ca2+ channel Orai, regulate intrinsic neuronal properties by control of developmental gene expression in flight-promoting central dopaminergic neurons (fpDANs). The fpDANs receive cholinergic inputs for release of dopamine at a central brain tripartite synapse that sustains flight (Sharma and Hasan, 2020). Cholinergic inputs act on the muscarinic acetylcholine receptor to stimulate intracellular Ca2+ release through the endoplasmic reticulum (ER) localised inositol 1,4,5-trisphosphate receptor followed by ER-store depletion and Orai mediated store-operated Ca2+ entry (SOCE). Analysis of gene expression in fpDANs followed by genetic, cellular, and molecular studies identified Orai-mediated Ca2+ entry as a key regulator of excitability in fpDANs during circuit maturation. SOCE activates the transcription factor Trithorax-like (Trl) which in turn drives expression of a set of genes including Set2, that encodes a histone 3 Lysine 36 methyltransferase (H3K36me3). Set2 function establishes a positive feedback loop, essential for receiving neuromodulatory cholinergic inputs and sustaining SOCE. Chromatin modifying activity of Set2 changes the epigenetic status of fpDANs and drives expression of key ion channel and signaling genes thus setting the excitability threshold that determines dopamine release for maintenance of long flight.