Seasonal influenza causes substantial morbidity and mortality in the United States. The U.S. Centers for Disease Control and Prevention (CDC) uses a compartmental framework to estimate the annual disease burden and burden prevented by vaccination for all influenza types and subtypes combined. However, these estimates do not capture underlying shifts in disease burden caused by different circulating influenza virus types or subtypes. We demonstrate an extension of the current framework to estimate disease burden and burden prevented by vaccination for influenza A virus subtypes A(H1N1) and A(H3N2), and influenza type B viruses. We applied this method to data from the 2016/17 to 2019/20 seasons that include age- and virus-specific hospitalizations and vaccine effectiveness estimates, and age-specific vaccination coverage estimates. We estimated the number of symptomatic illnesses, medically-attended illnesses, hospitalizations, and deaths caused by each virus, and the corresponding number prevented by vaccination. Disease burden and vaccine-prevented burden varied substantially by season, age, and virus type or subtype. The greatest disease burden was estimated in 2017/18, whereas 2019/20 had the greatest burden prevented by vaccination. Influenza A viruses contributed most to disease burden in all seasons. Vaccination against influenza B viruses prevented the largest percentage of hospitalizations among children and adults <65 years, whereas vaccination against A(H1N1) prevented the largest percentage of hospitalizations among adults ≥65 years. Overall, our results highlight complex variability in influenza disease burden by season, age, and virus type and subtype. These findings can be used to improve understanding of the factors impacting influenza disease burden each season and to enhance communications of the value of influenza vaccination.