NMDA receptors are glutamate-activated ion-channels that mediate fast excitatory transmission, synaptic plasticity and excitotoxicity. They assemble as heterotetramers of two NR1 and two NR2 subunits. Multiple isoforms with distinct kinetics, pharmacology and physiologic roles are differentially expressed in the central nervous system. Of these the NR1/NR2A and NR1/NR2B isoforms are most abundant. They are both inhibited by physiological proton concentrations but so far, the kinetic mechanism of proton inhibition has been characterized only for the NR1/NR2B isoform. To determine the mechanism of proton inhibition of NR1/NR2A receptors we recorded single-channel currents from cell-attached patches of HEK 293 cells transfected with NR1-1a, NR2A and GFP. The patch pipette contained saturating concentrations of glutamate and glycine and several proton concentrations in the range: pH 6.5 to 8.5. These records confirmed that protons do not change the channel's conductance and act solely by decreasing channel open probability (IC50 = 7.3). Kinetic analyses of our single-channel data showed that with increasing proton concentrations (pH 8, n = 5 vs. pH 6.5, n = 4) the mean channel open time decreased (7 ± 1.3 ms to 1.7 ± 3 ms) and the mean channel closed time increased (12 ± 0.1 ms to 94 ± 16 ms). To identify the rate constants affected by proton-binding we used best fit kinetic models to our single channel data. Results showed that similar to the mechanism previously reported for NR1-1a/NR2B receptors, protons inhibit NR1-1a/2A receptors by increasing the stability of two pre-open conformations. The rate constants we report here will help understand the role of protons in regulating synaptic transmission, plasticity and neuroprotection.