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Objectives The effect of a healthy lifestyle on the prognosis of neck pain is unknown. This study aimed to investigate if a healthy lifestyle behaviour influences the risk of long-duration troublesome neck pain among men and women with occasional neck pain. Design Longitudinal cohort study. Settings General population, and a subsample of the working population, in Stockholm County, Sweden. Participants This study involved 5342 men and 7298 women, age 18 to 84, from the Stockholm Public Health Cohort, reporting occasional neck pain at baseline in 2006. Measures Baseline information about leisure physical activity, smoking, alcohol consumption and consumption of fruits and vegetables were dichotomised into recommendations for healthy/not healthy behaviour. The exposure, a healthy lifestyle behaviour, was categorised into four levels according to the number of healthy behaviours (HB) met. Generalised linear models were applied to assess the exposure on the outcome long-duration troublesome neck pain (activity-limiting neck pain >= 2 days/week during the past 6 months), at follow-up in 2010. Results The adjusted risk of long-duration troublesome neck pain decreased with increasing adherence to a healthy lifestyle behaviour among both men and women (trend test: p<0.05). Compared with the reference category, none or one HB, the risk decreased by 24% (risk ratio 0.76, 95% CI 0.58 to 0.98) among men and by 34% (0.66, 0.54 to 0.81) among women, with three or four HBs. The same comparison showed an absolute reduction of the outcome by 3% in men (risk difference -0.03, 95% CI -0.05 to -0.01) and 5% in women (-0.05,-0.08 to -0.03). Similar results were found in the working population subsample. Conclusion Adhering to a healthy lifestyle behaviour decreased the risk of long-duration troublesome neck pain among men and women with occasional neck pain. The results add to previous research and supports the importance of promoting a healthy lifestyle behaviour.