Neuronal responses to stimuli rely on transcriptional programs controlled by histone proteins, including histone variants. Recent findings demonstrate that the variant H2BE promotes transcription and is critical for long-term memory, which relies on intact activity-dependent responses. However, whether H2BE is regulated by synaptic stimuli and controls activity-dependent responses remains to be determined. Here, we demonstrate that, unlike other variants, H2BE is depleted following long-term but not short-term increases in activity, indicating that its loss may promote homeostatic downscaling. Neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE-knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity. In summary, these data demonstrate that H2BE expression is inversely correlated with activity and is necessary for long-term activity-dependent scaling responses, revealing a mechanism through which histone variants control homeostatic plasticity in neurons.