Ca2+ release from internal stores is critical for mediating both normal and pathological intracellular Ca2+ signaling. Recent studies suggest that the inositol 1, 4, 5-triphosphate (IP3) receptor mediates Ca2+ release from internal stores upon cholinergic activation of the neuromuscular junction (NMJ) in both physiological and pathological conditions. Here we report that the type I IP3 receptor (IP3R1) -mediated Ca2+ release plays a crucial role in synaptic gene expression, development and neuromuscular transmission, as well as mediating degeneration during excessive cholinergic activation. We found that IP3R1-mediated Ca2+ release plays a key role in early development of the NMJ, in homeostatic regulation of neuromuscular transmission, and in synaptic gene expression. Reducing IP3R1-mediated Ca2+ release via siRNA knockdown or IP3R blockers in C2C12 cells decreased calpain activity, and prevented agonist-induced AChR cluster dispersal. In fully developed NMJ in adult muscle, IP3R1 knockdown or blockade effectively increased synaptic strength at pre- and postsynaptic sites, by increasing both quantal release and expression of AChR subunits and other NMJ-specific genes, in a pattern resembling muscle denervation. Moreover, in two mouse models of cholinergic overactivity and NMJ Ca2+ overload, anti-cholinesterase toxicity and the slow-channel myasthenic syndrome (SCS), IP3R1 knockdown eliminated NMJ Ca2+ overload, pathological activation of calpain and caspase proteases, and markers of DNA damage at subsynaptic nuclei, and improved both neuromuscular transmission and clinical measures of motor function. Thus, blockade or genetic silencing of muscle IP3R1 may be an effective and well-tolerated therapeutic strategy in SCS and other conditions of excitotoxicity or Ca2+ overload.