Neck pain and headache are two of the most common complications of whiplash injury. Therefore, we performed a systematic literature search on PubMed and Embase for publications reporting on the prevalence of neck pain and headache following whiplash injury. The literature search identified 2,709 citations of which 44 contained relevant original data. Of these, 27 studies provided data for the quantitative analysis. For non-population-based studies, the present meta-analysis showed that a pooled relative frequency of neck pain was 84% CI (68-95%) and a pooled relative frequency of headache was 60% (46-73%), within 7 days following whiplash injury. At 12 months post-injury, 38% (32-45%) of patients with whiplash still experienced neck pain, while 38% (18-60%) of whiplash patients reported headache at the same time interval post-injury. However, we also found considerable heterogeneity among studies with I-values ranging from 89-98% for the aforementioned meta-analyses. We believe that the considerable heterogeneity among studies underscores the need for clear-cut definitions of whiplash injury and standardized reporting guidelines for post-whiplash sequelae such as neck pain and headache. Future studies should seek to optimize these aspects paving the way for a better understanding of the clinical characteristics and natural course of whiplash-associated sequelae.