This systematic review aims to summarise the evidence from studies that examined morphometric alterations of the deep neck muscles using diagnostic imaging (ultrasound imaging, magnetic resonance imaging, and computed tomography) in patients diagnosed with primary headache disorders (PHD). No previous reviews have focused on documenting morphometric changes in this population. We searched five databases (up to 12 November 2022) to identify the studies. The risk of bias (RoB) was assessed using the Quality in Prognostic Studies (QUIPS) tool and the overall quality of the evidence was assessed using The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. A total of 1246 studies were screened and five were finally included; most were at high RoB, and the overall level of confidence in results was very low. Only two studies showed a significant association between morphometric alterations of the deep neck muscles and PHD (p < 0.001); nevertheless, their RoB was high. Contradictory and mixed results were obtained. The overall evidence did not show a clear association between morphometric alterations of the deep neck muscles in patients diagnosed with PHD. However, due to the limited number of studies and low confidence in the evidence, it is necessary to carry out more studies, with higher methodological quality to better answer our question.