Whole body vibration (WBV) is linked to short- and longer-term adverse health outcomes, including cognitive impairment, stress and memory loss, loss of balance, reduced proprioception, visual and vestibular disturbances, gastrointestinal problems, and musculoskeletal disorders. Epidemiological evidence supports the link between WBV and headache and head discomfort, but few experimental studies have examined this relationship, particularly with increased muscle tension, as an intermediary. This study aimed to investigate the relationship between muscle tension and vibration intensity, between perceived neck pain and headache/head discomfort and vibration intensity, and between muscle tension and reported neck pain and headache symptoms from simulated WBV based on field measurements of all-terrain vehicle operation on farm terrain. We observed significantly higher electromyography amplitude in the High condition (equivalent to EU Directive’s Exposure Limit Value) compared to both Low (equivalent to EU Directive’s Exposure Action Value) and Control (quiet sitting) conditions at the left upper trapezius muscle but there were no significant time effects. Neck pain and headache/head discomfort significantly increased after both Low (91% increase from baseline) and High (154% increase from baseline) vibration conditions but there were no significant differences between conditions. Based on simple regression modeling, the relationship between muscle activity and neck pain or headache was very weak (R2 = 0–0.093). Given the possibility of multiple factors contributing to headache symptoms, future research should not only consider the role of muscle tension but also sensory conflict, excessive noise, biodynamic responses, and a combination of these factors.