Chikungunya fever, a disease caused by chikungunya virus (CHIKV), reemerged and affected over 52,000 people in southern Thailand in 2008 and 2009. The CHIKV strain involved in this outbreak was the East Central South African (ECSA) strain with the E1-A226V mutation. The prevalence of CHIKV-associated chronic discomfort varied by virus lineage. This retrospective cohort study aims to describe the CHIKV-related symptoms persisting in CHIKV-affected patients, related factors, and the presence of anti-CHIKV immunoglobulin G (IgG) antibodies 5 years after the onset of disease. From 5,344 of the study population screened, a total of 89 affected patients reported persistent arthralgia 5 years after the disease onset (nonrecovery rate = 1.7%). Of the 141 affected patients enrolled, 122 cases (86.5%; 77 cases with persistent arthralgia and 45 cases of fully recovered) still had detectable levels of anti-CHIKV IgG antibodies. Long-term persistence of chronic joint symptoms is associated with the severity of the disease during the initial phase of the infection, but not gender, age, or comorbidities. The common manifestations were arthralgia (75.3%), morning joint stiffness (39.0%), muscle pain (19.5%), and occasional joint swelling (16.9%). Chronic joint symptoms could occur in either a fluctuating or a persistent manner and usually caused moderate pain. The joints affected were mainly fingers (71.4%), wrists (51.9%), and knees (50.6%). Most patients had polyarthralgia with symmetrical joint involvement. In some cases with persistent arthralgia, atypical manifestations, including severe depression with suicide attempts, severe weight loss, and severe hair loss, were found, and some patients still experienced severe joint pain.