Currently, evidence for effective physiotherapy interventions in patients with cervicogenic headache (CeH) is inconsistent. Although inter-individual variability in pain response is predictive for successful physiotherapy interventions, it was never explored in patients with CeH. Therefore the objective of the current study was to explore inter-individual variability in mechanical pain sensation, and its association with biopsychosocial-lifestyle (BPSL) characteristics in patients with CeH. A cross-sectional explorative analysis of inter-individual variability in mechanical pain sensation in 18 participants with CeH (29–51 years) was conducted. Inter-individual variability in mechanical pain sensation (standard deviations (SDs), F-statistics, Measurement System Analysis) was deducted from bilateral pressure pain thresholds of the suboccipitals, erector spine, tibialis anterior. BPSL-characteristics depression, anxiety, stress (Depression Anxiety Stress Scale-21), quality of life (Headache Impact Test-6), sleep-quality (Pittsburgh Sleep Quality Index), and sedentary time (hours/week) were questioned. Inter-individual variability in mechanical pain sensation explained 69.2% (suboccipital left), 86.8% (suboccipital right), 94.6% (erector spine left), 93.2% (erector spine right), 91.7% (tibialis anterior left), and 82% (tibialis anterior right) of the total variability in patients with CeH. The significant p-values and large F-statistic values indicate inter-individual differences in SDs. Significant associations between (1) lower quality of life and lower SDs of the suboccipital left PPT (p .005), and (2) longer sedentary time and higher SDs of the suboccipital left PPT (p .001) were observed. Results from our explorative study could suggest inter-individual variability in mechanical pain sensation at the left suboccipitals which associates with quality of life and sedentary time. These novel findings should be considered when phenotyping patients and ‘individually’ match interventions.