The aim of the study was to examine the influence of concomitant neck pain (NP) on the outcome of headache (HA) frequency and HA type in adolescence. A population-based sample of 13-year-olds with or without HA (n = 228) was followed for 3 years. NP was evaluated at the beginning of the follow-up on the basis of recorded muscle tenderness and self-reported symptoms. During the 3 years of follow-up, changes in both HA type and frequency were common. NP interfering with daily activities at the age of 13 years predicted change from non-frequent (0-1/month) to monthly HA (>1/month), especially in boys (P = 0.03 boys, P = 0.06 girls). The use of physiotherapy predicted persistence of monthly HA in boys (P = 0.004). The changes in HA type were not predictable by NP. In conclusion, the risk of worsening HA in adolescence is more probable if the HA is associated with NP interfering with daily activities.