Abstract Background Cost and quality-adjusted life-years (QALYs) gained by quadrivalent influenza vaccine (QIV) versus trivalent influenza vaccine (TIV) in Hong Kong elderly were estimated over 9 seasons. Methods TIV-unmatched influenza B infection rates with QIV versus TIV were estimated by an epidemiology model. Model parameters included percentages of influenza B lineages in circulation, influenza B-associated hospital admission, age-specific population, vaccine coverage and effectiveness. Incremental cost per QALY gained (ICER) by QIV versus TIV were estimated from Hong Kong’s societal perspective. Results Mean reduction in influenza B infection rate was 191.3 (95%CI 45.1-337.5) per 100,000 population aged ≥65 years. Highest cost savings and QALYs gained by QIV occurred in 2007 with high percentage of TIV-unmatched strain (92.9%) for age groups 65–79 years (USD266,473 and 22.8 QALYs) and ≥80 years (USD483,461 and 27.3 QALYs). ICERs of QIV were below willingness-to-pay for age group 65–79 years in 6, 5 and 3 years when QIV cost + USD1 + USD2 and + USD5 more than TIV, respectively. For age group ≥80 years, ICERs of QIV were below willingness-to-pay in 7 and 5 years when QIV cost + USD1 and + USD5, correspondingly. Conclusions Acceptance of QIV to be cost-effective in Hong Kong elderly was subject to QIV unit cost and percentage of circulating TIV-unmatched influenza B lineages.