Docking is the process during which the vesicle and pre-synaptic membrane line up in a fusion-ready state. Following docking, the membranes fuse to create a small opening which grows larger until the vesicle membrane collapses into the pre-synaptic membrane and exocytosis occurs. While the exact mechanisms behind synaptic fusion have not been determined in full, the process is known to be calcium dependent.

There is evidence that rab 3A and rab 3B, two G-proteins, guide synaptic vesicles to active zones. Once at the active zone, vesicle and plasma membrane proteins, with the assistance of cytoplasmic proteins, recognize each other and docking occurs. The cytoplasmic proteins, NSF and SNAPs, are involved in assuring proper vesicle targeting. NSF and SNAPs along with SNAP receptors (SNAREs) may form an initial complex between the vesicle and presynaptic membrane. Possible proteins on the vesicle membrane and pre-synaptic membrane that act as SNAREs are, respectively, synaptobrevin and syntaxin. These two proteins may allow the vesicle and presynaptic membrane to recognize each other.

Following docking, there is a second influx of calcium at the active zone, which causes the vesicle membrane to fuse to the presynaptic membrane, forming a temporary ion channel. This early fusion pore, similar to a gap junction, is a cytoplasmic bridge that connects the lumen of the vesicle with the space outside the neuronal terminal. The fusion pore is composed of two halves, one in the vesicle membrane and one in the pre-synaptic membrane. Proteins potentially involved in forming the fusion pore include synaptophysin on the vesicle membrane and physophilin on the pre-synaptic membrane. When aligned, these proteins may fuse the vesicle membrane to the pre-synaptic membrane. The formation of this pore is an energetically unfavorable event and, thus requires energy provided when NSF hydrolyzes ATP.

Without calcium influx, there is no fusion pore formed. There is evidence that the vesicle protein synaptotagmin is the key calcium sensor and plays a significant role in activating fusion. Synaptotagmin has membrane binding abilities, binds calcium, and has been observed in close proximity to the site of calcium influx. In the absence of calcium, synaptotagmin acts as a clamp and inhibits vesicle fusion; the vesicle remains in a fusion-ready state but does not form a fusion pore. Synaptotagmin acts as a calcium sensor and, with calcium influx, activates fusion. Synaptotagmin does not appear to participate in the actual fusion event but may pull the vesicle and pre-synaptic membrane into closer contact with each other or induce conformational changes in fusion proteins.

Once an initial pore is formed, it quickly dilates leading to exocytosis and neurotransmitter release. The vesicle membrane joins the plasma membrane and the contents of the vesicle are released into the synaptic cleft.