The goals of this study are to characterize the temporal dynamics of inter-regional connectivity of the brain in chronic headache (CH) patients versus their age/gender matched controls (CONCH, n = 28 pairs), and to determine whether dynamic measures reveal additional features to static functional connectivity and correlate with psychometric scores. Cortical thickness and inter-regional resting state fMRI connectivity were quantified and compared between CH and CONCH groups. Six cortical regions of interest (ROI) pairs that exhibited correlated cortical thickness and static functional connectivity abnormalities were selected for temporal dynamic analysis. Two methods were used: temporal sliding-window (SW) and wavelet transformation coherence (VVTC). SW analyses using three temporal windows of 30, 60, 120 s revealed that all six ROI pairs of CH exhibited higher percentage of strong connectivity (high r values), and smaller fast Fourier transform (FFT) amplitudes at a very low frequency range (i.e., 0.002-0.01 Hz), compared to those of CONCH. These features were particularly prevalent in the 120 s window analysis. Less variable dynamic fluctuation (i.e., smaller standard deviation of r values) was identified in two out of six ROI pairs in CH. WTC analysis revealed that time-averaged coherence was generally greater in CH than CONCH between wavelet decomposition scales 20 to 55 (0.018-0.05 Hz), and was statistically significant in three out of six ROI pairs. Together, the most robust and significant differences in temporal dynamics between CH and CONCH were detected in two ROI pairs: left medial-orbitofrontal left posterior-cingulate and left medial-orbitofrontal left inferior-temporal. The high degrees of sleep disturbance (high PSQI score), depression (high HRSD score) and fatigue (low SF-36 score) were associated with high degree of inter-regional temporal coherence in CH. In summary, these dynamic functional connectivity (dFC) measures uncovered a temporal "lock-down" condition in a subset of ROI pairs, showing static functional connectivity changes in CH patients. This study provides important evidence for the presence of associated psychological wellbeing and abnormal temporal dynamics in between specific cortical regions in CH patients. (C) 2016 Elsevier Inc. All rights reserved.