The speed and reliability of neuronal reactions are important factors for proper functioning of the nervous system. To understand how organisms use protein molecules to carry out very fast biological actions, we quantified single-molecule reaction time and its variability in synaptic transmission. From the synaptic delay of crayfish neuromuscular synapses the time for a few Ca2+ ions to bind with their sensors in evoked neurotransmitter release was estimated. In standard crayfish saline at room temperature, the average Ca2+ binding time was 0.12 ms for the first evoked quanta. At elevated extracellular Ca2+ concentrations this binding time reached a limit due to saturation of Ca2+ influx. Analysis of the synaptic delay variance at various Ca2+ concentrations revealed that the variability of the Ca2+-sensor binding time is the major source of the temporal variability of synaptic transmission, and that the Ca2+-independent molecular reactions after Ca2+ influx were less stochastic. The results provide insights into how organisms maximize reaction speed and reliability.