In March 2024, CDC released symptom-based isolation guidance for viral respiratory illnesses including influenza: isolation from others until fever-free for 24 hours and other symptoms are improving, followed by 5 days of post-isolation precautions. This study evaluated how well these recommendations aligned with influenza virus RNA shedding and assessed self-reported isolation in a multi-site household study during 2023–2025. We analyzed data from 1294 participants with influenza, including 627 with a clear peak in viral RNA levels and symptom resolution during follow-up. Participants provided daily symptom diaries and nasal swabs. We used Kaplan–Meier models to estimate recommended isolation duration based on CDC guidelines and compared this to viral RNA shedding measured by cycle threshold values and viral loads. The median recommended isolation duration was 6 days (interquartile range 4–7). Peak viral RNA shedding occurred a median of 4 days post-symptom onset, falling during recommended isolation for 80% (by Ct) and 69% (by viral load) of participants and increasing to 100% and 97% respectively by day 6 post-isolation. However, only 21% reported isolating from household members (median 2 days), and 80% isolated from the community (median 4 days). These findings support symptom-based isolation and emphasize the importance of post-isolation precautions.