All four HCN subunits are expressed in the brain. In addition to their proposed roles in pacemaking rhythmic or oscillatory activity, HCN channels may control the way that neurons respond to synaptic input. Initial studies suggest roles for HCN channels in sour taste, coordinated motor behavior and aspects of learning and memory. Clinically, there is evidence that HCN channels play roles in epilepsy and neuropathic pain.  HCN channels have been shown to be important for activity-dependent mechanisms for olfactory sensory neuron growth.
HCN1 and 2 channels have been found in dorsal root ganglia, basal ganglia, and the dendrites of neurons in the hippocampus. It has been found that human cortical neurons have particularly high amount of HCN1 channel expression in all layers. HCN channel trafficking along dendrites in the hippocampus of rats has shown that HCN channels are quickly shuttled to the surface in response to neural activity. HCN channels have also been observed in the retrotrapezoid nucleus (RTN), a respiratory control center that responds to chemical signals such as CO. When HCN is inhibited, serotonin fails to stimulate chemoreceptors in the RTN. This illustrates a connection between HCN channels and respiratory regulation. Due to the complex nature of HCN channel regulation, as well as the complex interactions between multiple ion channels, HCN channels are fine-tuned to respond to certain thresholds and agonists. This complexity is believed to affect neural plasticity.