The cervical cancer burden in Lithuania has remained high, and there are no previous effectiveness studies of cervical cancer prevention programme in the country. We investigated the effect of a prevention programme on the risk of mortality from cervical cancer in Lithuania by conducting a mortality audit study. The register-based case-control study included 715 cervical cancer deaths that occurred during 2010-2015 in Lithuania and their 2145 matched controls. Screening histories for cases and controls were obtained from the National Health Insurance Fund database. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using conditional logistic regression and corrected for self-selection bias. Index screening was associated with a 56% reduction in the cervical cancer death risk, OR: 0.44; 95% CI 0.26-0.74. The ORs for stage I and stage II+ cancers were 0.80; 95% CI 0.32-2.00 and 0.36; 95% CI 0.21-0.62, respectively. The preventive effect was statistically significant for women aged ≥40 years, while nonsignificant for younger. In women who died of cervical cancer, 71% were not invited and 88% were not screened within the recommended 36 months prior to index date. Among cases with index invitation, 32% had index screening compared to 70% in controls. In conclusion, participation in screening has been effective in reducing cervical cancer mortality in Lithuania. The study shows poor screening attendance, emphasizing the importance of greater efforts at the national level to improve the effectiveness of the screening.