Body aches with the flu typically last about 3 to 5 days. These aches are part of the most severe symptoms phase, which usually occurs in the first few days of illness. While the intense body aches usually improve after this period, other symptoms such as cough and fatigue can linger for 1 to 2 weeks or more. Most people start feeling notably better by day 5 to 6 and generally recover within 1 to 2 weeks, though some residual tiredness may persist even longer.