Introduction In Lithuania, breast cancer (BC) is the most common non-cutaneous cancer and the most common cancer death among women. The aim of this study was to determine the influence of SES on female BC incidence, mortality and survival during the period 2001–2009, using population-based census-linked registry data covering the entire population of Lithuania. Methods The study was based on a census-linked dataset which is based on the linkage of all cancer cases from the Lithuanian Cancer Registry (cancer incidence) and all deaths and emigration records from the Statistics Lithuania for the period 6 April 2001–31 December 2009 to the 2001 population census records at the beginning of the follow-up period (6 April 2001). Emigration records were needed in order to estimate population exposures under risk. The population under study included all of the permanent residents of Lithuania aged 30–74 years on the census day (6 April 2001). Information about urban-rural place of residence and education was taken from census records. Education was classified according to three broad categories of completed education: higher education (at least 14 years of schooling), secondary education (10–13 years of schooling), and lower than secondary education (up to 9 years of schooling). Incidence rate ratios (IRR) and mortality rate ratios (MRR) by education and urban-rural residence were estimated by means of multivariate Poisson regression models controlling for age and using higher education and urban place of residence as reference categories using higher education and urban as a reference category. In order to calculate relative survival rates, life tables for the general population by each educational category and each place of residence were calculated using the same census-linked dataset (cumulative five-year survival rates for the period 2001–2009 were estimated). The expected survival estimates were derived using the Ederer II method. STATA statistical software was used to calculate relative survival and avoidable deaths. Results IRRs showed substantial and statistically significant inverse effects of education and place of residence. The lowest risk of BC was observed in the group of women with lower than secondary education (0.63 times, CI: 0.59–0.67) and in rural areas (0.77 times, CI: 0.73–0.80). Statistically significant lower risk was also observed in the secondary education group (0.80 times, CI: 0.76–0.84), as compared to the higher education. Mortality rates ratios also showed a statistically significant inverse educational mortality gradient. The lowest MRRs were in women with lower than secondary education (0.87 times, CI: 0.79–0.96). There were no significant differences in MRRs by place of residence. We found the same inverse gradient in BC survival, with the worst survival indicators in the lower than secondary education group. Survival rates were significantly decreasing with decreasing education. Five-year relative survival in the higher education group was 80.2%. The absolute difference in survival rates between the highest and the lowest educational groups was 15.3%. The study found a moderate disadvantage in survival among rural women. The same gradient was observed by place of residence too. Conclusions The higher risk of BC in the highest SES in Lithuania corresponds to the results from other countries. For BC, the risk gradient may be explained by other well-established breast cancer risk factors such as postponement of childbearing and low parity which are also more common among females with high SES in Lithuania. Higher SES women are also more likely to obtain routine mammography screening due to better access to preventive healthcare, thereby increasing the detection of breast cancer in this group. SES differences in access to healthcare, modern treatment, as well as inequalities in time of diagnosis may explain the observed differences in BC survival.