Chemical proteomics can provide global portraits of small molecule-protein interactions in native biological systems. However, such ligandability maps have, to date, mostly been restricted to readily accessible cancer cell lines or primary immune cells. Here, we describe an activity-based protein profiling (ABPP) strategy for mapping the covalent ligandability of primary brain cells freshly isolated from mice. By investigating sets of stereochemically defined electrophilic small molecules ("stereoprobes"), we identify liganding events for diverse proteins, including many with nervous system-enriched expression profiles. In this category were multiple hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which we show are covalently liganded by tryptoline acrylamide stereoprobes at a conserved cysteine in their cyclic nucleotide-binding domain. The stereoprobes were found to block cAMP-dependent shifts in voltage dependence while sparing basal HCN channel activity. Our work describes an advanced ABPP platform for identifying ligands targeting nervous system-enriched proteins, including chemical probes for modulating HCN channel function in cells.