Cognitive decline with age is associated with brain atrophy and reduced brain activations, but the underlying neurophysiological mechanisms are unclear, especially in deeper brain structures primarily affected by healthy aging or neurodegenerative processes. Here, we characterize time-resolved, resting-state magnetoencephalography activity of the hippocampus and subcortical brain regions in a large cohort of healthy young and older volunteers from the Cam-CAN open repository. The data show age-related changes in both rhythmic and arrhythmic signal strength and temporal variability in multiple deeper brain regions, including the hippocampus, striatum, and thalamus. We observe a slowing of neural activity in deeper brain regions, which echoes previous reports of cortical slowing. We also report reduced occipito-parietal alpha peak associated with increased theta-band activity and signal variability in the hippocampus, an effect that may reflect compensatory processes as theta activity and variability were more strongly expressed when cognitive performances are preserved. Overall, this study advances the understanding of the biological nature of inter-individual variability in aging. The data provide new insight of how hippocampus and subcortical neurophysiological activity evolve with biological age, and highlight frequency-specific effects associated with cognitive decline vs. cognitive maintenance.