The objective of the study was to find out what kind of neck pain (NP) is associated with headache (HA) and with various headache variables: frequency, type, intensity, disturbance, and relief with analgesics. A population-based sample of 12-year-olds with and without HA (n = 304) was followed for 4 years. At the age of 16 years, NP was evaluated on the basis of self-reported symptoms and a thorough physical examination of the neck region. Both self-reported and measured NP were associated with HA variables. Co-occurrent NP was found in adolescents with migraine as often as in those with tension-type HA. Especially, muscle pain and intensive, frequent NP were associated with disturbing HA unresponsive to analgesics. The study indicates that concomitant NP should be considered in adolescent HA sufferers, and a thorough cervical and muscle evaluation is recommended when planning the treatment of HA.