Neuronal preconditioning is a phenomenon where a previous exposure to a sub‐lethal stress stimulus increases the resistance of neurons towards a second, normally lethal stress stimulus. Activation of the energy stress sensor, AMP‐activated protein kinase (AMPK) has been shown to contribute to the protective effects of ischaemic and mitochondrial uncoupling‐induced preconditioning in neurons, however, the molecular basis of AMPK‐mediated preconditioning has been less well characterized. We investigated the effect of AMPK preconditioning using 5‐aminoimidazole‐4‐carboxamide riboside (AICAR) in a model of NMDA‐mediated excitotoxic injury in primary mouse cortical neurons. Activation of AMPK with low concentrations of AICAR (0.1 mM for 2 h) induced a transient increase in AMPK phosphorylation, protecting neurons against NMDA‐induced excitotoxicity. Analysing potential targets of AMPK activation, demonstrated a marked increase in mRNA expression and protein levels of the anti‐apoptotic BCL‐2 family protein myeloid cell leukaemia sequence 1 (MCL‐1) in AICAR‐preconditioned neurons. Interestingly, over‐expression of MCL‐1 protected neurons against NMDA‐induced excitotoxicity while MCL‐1 gene silencing abolished the effect of AICAR preconditioning. Monitored intracellular Ca2+ levels during NMDA excitation revealed that MCL‐1 over‐expressing neurons exhibited improved bioenergetics and markedly reduced Ca2+ elevations, suggesting a potential mechanism through which MCL‐1 confers neuroprotection. This study identifies MCL‐1 as a key effector of AMPK‐induced preconditioning in neurons.