Influenza-associated mortality has not been quantified in the Philippines. Here, we constructed multiple negative binomial regression models to estimate the overall and age-specific excess mortality rates (EMRs) associated with influenza in the Philippines from 2006 to 2015. The regression analyses used all-cause mortality as the dependent variable and meteorological controls, time, influenza A and B positivity rates (lagged for up to two time periods), and annual and semiannual cyclical seasonality controls as independent variables. The regression models closely matched observed all-cause mortality. Influenza was estimated to account for a mean of 5,347 excess deaths per year (1.1% of annual all-cause deaths) in the Philippines, most of which (67.1%) occurred in adults aged ≥60 years. Influenza A accounted for 85.7% of all estimated excess influenza deaths. The annual estimated influenza-attributable EMR was 5.09 (95% CI: 2.20-5.09) per 100,000 individuals. The EMR was highest for individuals aged ≥60 years (44.63 [95% CI: 4.51-44.69] per 100,000), second highest for children aged less than 5 years (2.14 [95% CI: 0.44-2.19] per 100,000), and lowest for individuals aged 10 to 19 years (0.48 [95% CI: 0.10-0.50] per 100,000). Estimated numbers of excess influenza-associated deaths were considerably higher than the numbers of influenza deaths registered nationally. Our results suggest that influenza causes considerable mortality in the Philippines-to an extent far greater than observed from national statistics-especially among older adults and young children.