Background Prior studies demonstrate that ethanol (EtOH) exposure induces the release of intracellular calcium (CA2+) in modulation of γ‐aminobutyric acid‐ergic tone and produces concomitant alterations in sigma (σ)‐1 protein expression that may contribute to the development EtOH dependence. However, the influence of CA2+ released from endoplasmic reticulum (ER)‐bound inositol triphosphate (IP3) and σ‐1 receptors in regulating hippocampal function has yet to be delineated. Methods Rat hippocampal explants were subjected to chronic intermittent EtOH (CIE) exposure with or without the addition of IP3 inhibitor xestospongin C (0 to 0.5 μM) or σ‐1 receptor antagonist BD‐1047 (0 to 80 μM). Hippocampal viability was assessed via immunohistochemical labeling of neuron‐specific nuclear protein (NeuN)/Fox‐3 in CA1, CA3, and dentate gyrus (DG) subregions. Results Exposure to CIE produced consistent and significant decreases of NeuN/Fox‐3 in each primary cell layer of the hippocampal formation. Co‐exposure to xestospongin reversed these effects in the CA1 subregion and significantly attenuated these effects in the CA3 and DG regions. Xestospongin application also significantly increased NeuN/Fox‐3 immunofluorescence in EtOH‐naïve hippocampi. Co‐exposure to 20 μM BD‐1047 also reversed the loss of NeuN/Fox‐3 during CIE exposure in each hippocampal cell layer, whereas exposure to 80 μM BD‐1047 did not alter NeuN/Fox‐3 in EtOH‐treated hippocampi. By contrast, 80 μM BD‐1047 application significantly increased NeuN/Fox‐3 immunofluorescence in EtOH‐naïve hippocampi in each subregion. Conclusions These data suggest that EtOH stimulates ER IP3 and σ‐1 receptors to promote hippocampal loss of NeuN/Fox‐3 during CIE. These findings suggest that, while exposed to ethanol, endoplasmic reticulum (ER)‐bound inositol triphosphate (IP3) and sigma (σ)‐1 receptors work cooperatively to promote mobilization of calcium from intracellular stores into the cytosol. This is demonstrated by the ability of xestospongin C and BD 1047, respectively, to reverse ethanol‐associated changes promoting withdrawal effects. This calcium mobilization contributes to neuroadaptions to prolonged ethanol exposure that promote a well‐characterized glutamatergic receptor‐mediated ethanol withdrawal‐induced excitotoxic cascade in the hippocampus.