Despite the relatively low breast cancer incidence in Estonia, mortality remains high, and participation in mammography screening is below the recommended 70%. The objective of this register-based study was to evaluate incidence-based (IB) breast cancer mortality before and after the introduction of organized mammography screening in 2004. Breast cancer deaths individually linked to breast cancer diagnosis were obtained from the Estonian Cancer Registry and used for calculating IB mortality. We compared age-specific IB mortality rates across 5-year birth cohorts and 5-year periods. Poisson regression was used to compare IB mortality for one age group invited to screening (50-63) and three age groups not invited to screening (30-49, 65-69, and 70+) during two periods before and after screening initiation (1993-2003 and 2004-2014). Joinpoint regression was used for age-standardized incidence and IB mortality trends. Age-standardized IB mortality has been decreasing since 1997. Age-specific IB mortality for birth cohorts never exposed to screening showed a continuous increase with age, while in cohorts exposed to organized screening the mortality curve flattened or declined after the age of first invitation. Significant decreases in mortality from 1993-2003 to 2004-2014 were seen in the 30-49 (age-adjusted rate ratio 0.51, 95% CI 90.42-0.63) and 50-63 (0.65, 95% CI 0.56-0.74) age groups, while no decline was seen in the 65-69 and 70+ age groups. The age specific IB mortality curves in birth cohorts exposed to screening and the significant mortality decline in the target age group after the initiation of the organized program suggest a beneficial effect of screening. Improved treatment without screening has not reduced mortality in older age groups. Our results support raising the upper screening age limit to 74 years.