Background Little is known about the persistence and impact of non-rheumatic symptoms after acute chikungunya disease. We have studied the clinical presentation and long-term impact of rheumatic and non-rheumatic symptoms on health related quality of life (QoL) 2.5 years after disease onset. Additionally, the validity of the Curaçao Long-Term Chikungunya Sequelae (CLTCS) score in classifying disease severity over time was evaluated. Methodology/Principal findings This prospective cohort study followed 248 chikungunya patients. Symptoms and SF-36 QoL were evaluated during baseline and follow-up at 2.5 years using questionnaires. Chikungunya disease status was classified using the CLTCS-score. At 2.5 years after disease onset patients were classified as being recovered (43%), mildly (35%) or highly (22%) affected. In comparison to mildly affected, highly affected patients reported the highest prevalence of ongoing rheumatic and non-rheumatic/psychological symptoms, with increased prevalence of arthralgia in the lower extremities (p = .01) and fatigue (p = .049) over time, and higher pain intensity (p < .001). Compared to mildly affected, being highly affected was associated with weakness in the lower extremities (OR: 1.90; CI: 1.29–2.80, p = .001) and worsened physical and mental QoL impairment. Conclusions Patients are both physically and psychologically affected by rheumatic and non-rheumatic symptoms of long-term chikungunya disease. The CLTCS-score is an easy to use instrument for classifying long-term chikungunya disease severity and impact and can facilitate health care providers in identifying highly affected patients who are prone to develop severe QoL impairment. Highly affected patients are recommended to be treated in a multidisciplinary setting to improve physical and psychological functioning, and QoL.