Fatigue and pain are both prevalent and frequently co-occur. No standard measure of fatigue exists, but most definitions include a continuum between high levels of energy and fatigue. There is limited knowledge about the course of fatigue in the general population and its association with functioning and other health outcomes. Our main aim was to identify trajectories of energy and fatigue in the general population and to investigate whether chronic pain is related to a negative prognosis of chronic fatigue. Longitudinal latent class analysis was performed to classify 4771 individuals into trajectory groups based on five quarterly repeated measures. A five-cluster solution was identified: 'much energy' (n = 1471, [31%]), 'varying energy' (n = 1445, [30%]), 'some energy' (n = 921, [19%]), 'low energy' [chronic moderate fatigue] (n = 852, [18%]) and 'no energy'[chronic severe fatigue] (n = 82, [2%]). Individuals with chronic moderate fatigue who reported chronic pain had reduced probability of improvement over the following 3 years (OR = 0.67, 95% CI [0.52, 0.88]). Chronic fatigue is highly prevalent in the general population and a small proportion have chronic severe fatigue. When chronic pain co-occurs with chronic fatigue, improvement of chronic fatigue is less likely, indicating that these symptoms may perpetuate each other. Understanding the close relationship between chronic pain and chronic fatigue is important as they both contribute to suffering and loss of functioning, may be related to the same underlying diseases, or in the absence of disease, may share common mechanisms. This study highlights the important role of chronic pain in relation to chronic fatigue, both by showing a strong association between the prevalence of the two conditions, and by showing that chronic pain is associated with a negative prognosis of chronic fatigue.