The M-current is a voltage-gated potassium current generated by channels composed by KCNQ2-5 subunits. The pedunculopontine nucleus (PPN) is part of the Reticular Activating System (RAS), associated with sleep regulation. As little is known about the composition, subcellular location and physiological implication of the M-current in PPN, our aim was to demonstrate the presence of KCNQ4 in the PPN, and its contribution to the neuronal function of this nucleus. We used a transgenic mouse lacking KCNQ4 expression (KO) and one with fluorescent-labeled cholinergic neurons (tdTomatoStop+ChAT::Cre). Using qPCR, immunofluorescence and electrophysiology on brain slices, we demonstrated that only a subpopulation of cholinergic neurons (around 27%), located on the external limits of the PPN has KCNQ4-mediated M-current. We also found that KCNQ4 regulates the expression of other KCNQ subunits. In KO mice, the expression profile changed drastically respect with the WT: Kcnq2 expression decreased, Kcnq3 increase and Kcnq5 disappeared. To study the influence of KCNQ4 on circadian rhythm we used behavioral testing. KO mice exhibited alterations in the activity cycles showing a higher sensitivity to changes in the light-darkness cycles. In summary, we found that some PPN cholinergic neurons have KCNQ4-dependent M-current and this subunit contributes to modulate the circadian rhythm. Since the PPN is affected in certain neurological diseases, KCNQ4 might be a potential pharmacological target.