Influenza is a viral infection which is quite common, but which can produce quite severe symptoms, including fever, sore throat, and aches and pains of muscles and joints. Most of these symptoms should go away gradually after the infection clears, but sometimes with viral infections like influenza there can be a condition called reactive arthritis
which develops after the infection clears.
In reactive arthritis, one or several joints may be very painful and swollen. The condition is probably related to how the nonspecific revving up of your immune system by the infection causes inflammation in joints. If you have significant joint pain
or swelling or stiffness, you should definitely talk to your primary care doctor
Most cases of reactive arthritis will resolve slowly on their own. Often taking regular anti inflammatory medications like ibuprofen or naprosyn can help, and your doctor can advise you on what a good dose of these medications would be. More severe cases of reactive arthritis may require higher doses of anti inflammatory medicines or even other classes of medicines to dampen down the immune system's response.
Talk to your doctor, who will be able to confirm a diagnosis and discuss what is the right treatment for your case.