Aim To investigate the presence of fatty infiltrate in the cervical extensor musculature in patients with insidious-onset neck pain to better understand the possible pathophysiology underlying such changes in chronic whiplash-associated disorders (WAD). Materials and methods A sample of convenience of 23 women with persistent insidious-onset neck pain (mean age 29.2 ᠶ.9 years) was recruited for the study. Magnetic resonance imaging (MRI) was used to quantify fatty infiltration in the cervical extensor musculature. Quantitative Sensory Testing (QST; pressure and thermal pain thresholds) was performed as sensory features are present in chronic whiplash. Self-reported pain and disability, as well as psychological distress, were measured using the Neck Disability Index (NDI) and the General Health Questionnaire-28 (GHQ-28), respectively. Results Measures were compared with those of a previous dataset of chronic whiplash patients (n = 79, mean age 29.7 ᠷ.8 years). Using a classification tree, insidious-onset neck pain was clearly identified from whiplash (p < 0.001), based on the presence of MRI fatty infiltrate in the cervical extensor musculature (0/102 individuals) and altered temperature thresholds (cold; 3/102 individuals). Conclusion Fatty infiltrates in the cervical extensor musculature and widespread hyperalgesia were not features of the insidious-onset neck pain group in this study; whereas these features have been identified in patients with chronic WAD. This novel finding may enable a better understanding of the underlying pathophysiological processes in patients with chronic whiplash.