ObjectiveIn this pilot prospective cohort study, we aimed to evaluate, using high‐density electroencephalography (HD‐EEG), the longitudinal changes in functional connectivity (FC) in patients with chronic migraine (CM) treated with onabotulinumtoxinA (OBTA).BackgroundOBTA is a treatment for CM. Several studies have shown the modulatory action of OBTA on the central nervous system; however, research on migraine is limited.MethodsThis study was conducted at the Neurology Unit of “Policlinico Tor Vergata,” Rome, Italy, and included 12 adult patients with CM treated with OBTA and 15 healthy controls (HC). Patients underwent clinical scales at enrollment (T0) and 3 months (T1) from the start of treatment. HD‐EEG was recorded using a 64‐channel system in patients with CM at T0 and T1. A source reconstruction method was used to identify brain activity. FC in δ‐θ‐α‐β‐low‐γ bands was analyzed using the weighted phase‐lag index. FC changes between HCs and CM at T0 and T1 were assessed using cross‐validation methods to estimate the results’ reliability.ResultsCompared to HCs at T0, patients with CM showed hyperconnected networks in δ (p = 0.046, area under the receiver operating characteristic curve [AUC: 0.76‐0.98], Cohen's κ [0.65‐0.93]) and β (p = 0.031, AUC [0.68‐0.95], Cohen's κ [0.51‐0.84]), mainly involving orbitofrontal, occipital, temporal pole and orbitofrontal, superior temporal, occipital, cingulate areas, and hypoconnected networks in α band (p = 0.029, AUC [0.80‐0.99], Cohen's κ [0.42‐0.77]), predominantly involving cingulate, temporal pole, and precuneus. Patients with CM at T1, compared to T0, showed hypoconnected networks in δ band (p = 0.032, AUC [0.73‐0.99], Cohen's κ [0.53‐0.90]) and hyperconnected networks in α band (p = 0.048, AUC [0.58‐0.93], Cohen's κ [0.37‐0.78]), involving the sensorimotor, orbitofrontal, cingulate, and temporal cortex.ConclusionThese preliminary results showed that patients with CM presented disrupted EEG‐FC compared to controls restored by a single session of OBTA treatment, suggesting a primary central modulatory action of OBTA.