Objective The purpose of this study was to investigate the immediate effects of head-neck massage on heart rate variability (HRV), mood states, and pressure pain thresholds (PPTs) in patients with chronic tension-type headache (CTTH). Methods Eleven patients (8 females), between 20 and 68 years old, with CTTH participated in this crossover study. Patients received either the experimental treatment (massage protocol) or a placebo intervention (detuned ultrasound). Holter electrocardiogram recordings (standard deviation of the normal-to-normal interval, square root of mean squared differences of successive NN intervals, index HRV, low-frequency component, and high-frequency component), PPT over both temporalis muscles, and Profile of Mood States questionnaire (tension-anxiety, depression-dejection, anger-hostility, vigor, fatigue, confusion) were obtained preintervention, immediately after intervention, and 24 hours postintervention. Self-reported head pain was also collected preintervention and 24 hours postintervention. Separate analyses of covariance (ANCOVAs) were performed with each dependent variable. The hypothesis of interest was group × time interaction. Results The ANCOVA showed a significant group × time interaction for index HRV (F = 4.5, P = .04), but not for standard deviation of the normal-to-normal interval (F = 1.1, P = .3), square root of mean squared differences of successive NN intervals (F = 0.9, P = .3), low-frequency component (F = 0.03, P = .8), or high-frequency component (F = 0.4, P = .5) domains. Pairwise comparisons found that after the manual therapy intervention, patients showed an increase in the index HRV ( P = .01) domain, whereas no changes were found after the placebo intervention ( P = .7). The ANCOVA also found a significant group × time interaction for tension-anxiety (F = 5.3, P = .03) and anger-hostility (F = 4.6, P = .04) subscales. Pairwise comparisons found that after the manual therapy intervention, patients showed a decrease in tension-anxiety ( P = .002) and anger-hostility ( P = .04) subscales, whereas no changes were found after the placebo intervention ( P > .5 both subscales). No significant changes were found in PPT levels (right F = 0.3, P = .6, left F = 0.4, P = .5). A significant group × time interaction for pain (F = 4.8, P = .04) was identified. No influence of sex was found (F = 1.5, P = .3). Pairwise comparisons showed that head pain (numerical pain rating scale) decreased 24 hours after manual therapy ( P < .05) but not after the placebo intervention ( P = .9). Conclusions The application of a single session of manual therapy program produces an immediate increase of index HRV and a decrease in tension, anger status, and perceived pain in patients with CTTH.