Disrupted synaptic inhibition is implicated in most psychiatric disorders, yet the molecular mechanisms that shape and sustain inhibitory synapses are poorly understood. Here, we find that the function of a subset of inhibitory synapses in brain is controlled by binding of presynaptic Neurexin-3 to postsynaptic dystroglycan, adhesion molecules that are associated with cognitive impairments. We found that Neurexin-3 alternative splicing at two sites, SS2 and SS4, acts as an ‘and/or’ logic gate to regulate the release probability, but not the number, of inhibitory synapses in olfactory bulb and prefrontal cortex. The same SS2 and SS4 splice variants that enable inhibitory synapse function also allow binding of Neurexin-3 to dystroglycan. Inactivation of postsynaptic dystroglycan, in turn, produces a similar decrease in release probability as the presynaptic Neurexin-3 deletion. Furthermore, a minimal dystroglycan-binding construct of Neurexin-3 fully sustains inhibitory synaptic function, suggesting that trans-synaptic dystroglycan binding is not only necessary but also sufficient for inhibitory synapse function. Thus, Neurexin-3 enables a normal release probability at inhibitory synapses via a trans-synaptic feedback loop requiring binding of presynaptic Neurexin-3 to postsynaptic dystroglycan.