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The incubation period of chikungunya disease ranges from 2 to 12 days, typically two to three. The majority of those infected will develop symptoms.[11] Symptoms include a fever up to 40 °C (104 °F), petechial or maculopapular rash of the trunk and occasionally the limbs, and arthralgia or arthritis affecting multiple joints.[12] Other nonspecific symptoms can include headache, nausea, vomiting, conjunctivitis, slight photophobia, and partial loss of taste.[13] Ocular inflammation from chikungunya may present as iridocyclitis, or uveitis. Retinal lesions may also occur.[14] Swelling of legs is observed in many people, the cause of which remains obscure as it is not related to any cardiovascular, renal, or hepatic abnormalities. Typically, the fever lasts for two days and then ends abruptly. However, other symptoms, namely joint pain, intense headache, insomnia and an extreme degree of prostration, last for a variable period, usually about five to seven days.[12] People have complained of joint pains for much longer time periods, some as long as two years, depending on their age.[15][16] Recovery from the disease varies by age. Younger people recover within five to 15 days; middle-aged people recover in 1.0 to 2.5 months. Recovery is longer for the elderly. The severity of the disease, as well as its duration, is less in younger people and pregnant women. In pregnant women, no untoward effects are noticed after the infection.

Observations during recent epidemics have suggested chikungunya may cause long-term symptoms following acute infection. During the La Reunion outbreak in 2006, more than 50% of subjects over the age of 45 reported long-term musculoskeletal pain[17] with up to 60% of people reporting prolonged arthralgia three years following initial infection.[18] A study of imported cases in France reported that 59% of people still suffered from arthralgia two years after acute infection.[19] Following a local epidemic of chikungunya in Italy, 66% of people reported muscles pains, joint pains, or asthenia at one year after acute infection.[20] Long-term symptoms are not an entirely new observation; long-term arthritis was observed following an outbreak in 1979.[21] Common predictors of prolonged symptoms are increased age and prior rheumatological disease.[17][18][20][22] The cause of these chronic symptoms is currently not fully known. Markers of autoimmune or rheumatoid disease have not been found in people reporting chronic symptoms.[18][23] However, some evidence from humans and animal models suggests chikungunya may be able to establish chronic infections within the host. Viral antigen was detected in a muscle biopsy of a people suffering a recurrent episode of disease three months after initial onset.[24] Additionally, viral antigen and RNA were found in synovial macrophages of a person during a relapse of musculoskeletal disease 18 months after initial infection.[25] Several animal models have also suggested chikungunya virus may establish persistent infections. In a mouse model, viral RNA was detected specifically in joint-associated tissue for at least 16 weeks after inoculation, and was associated with chronic synovitis.[26] Similarly, another study reported detection of a viral reporter gene in joint tissue of mice for weeks after inoculation.[27] In a nonhuman primate model, chikungunya virus was found to persist in the spleen for at least six weeks.[28]

The most effective means of prevention are protection against contact with the disease-carrying mosquitoes and mosquito control.[9] These include using insect repellents with substances such as DEET (N,N-diethyl-meta-toluamide; also known as N,N'-diethyl-3-methylbenzamide or NNDB), icaridin (also known as picaridin and KBR3023), PMD (p-menthane-3,8-diol, a substance derived from the lemon eucalyptus tree), or IR3535. Wearing bite-proof long sleeves and trousers also offers protection. In addition, garments can be treated with pyrethroids, a class of insecticides that often has repellent properties. Vaporized pyrethroids (for example in mosquito coils) are also insect repellents. Securing screens on windows and doors will help to keep mosquitoes out of the house. In the case of the day-active A. aegypti and A. albopictus, however, this will have only a limited effect, since many contacts between the mosquitoes and humans occur outside.