Purpose: In this study, we analyzed the mortality and survival of colorectal cancer patients in Lithuania. Methods: This was a national cohort study. Population-based data from the Lithuanian Cancer Registry and period analyses were collected. Overall, 20,980 colorectal cancer patients were included. We examined the changes in colorectal cancer mortality and survival rates between 1998 and 2012 according to cancer anatomical sub-sites and stages. We calculated the 5-year relative survival estimates using period analysis. Results: Overall, 20,980 colorectal cancer cases reported from 1998 to 2012 were included in the study. The total number of newly diagnosed colorectal cancers increased from 1998–2002 to 2008–2012 by 12.1%. The highest number of colorectal cancers was localized and increased from 33.9% to 42.0%. The number of cancers with regional metastases and advanced cancers decreased by 11.1% and 15.5%, respectively. An increased number of new cases was observed for almost all colon cancer sub-sites. The overall 5-year relative survival rate increased from 37.9% in 1998–2002 to 51.5% in 2008–2012. We showed an increase in survival rates for all stages and all sub-sites. In the most recent period, patients with a localized disease had a 5-year survival rate of 78.6%, while survival estimates for advanced cancer patients remained low at 6.6%. Conclusion: Although survival rates variated in colorectal cancer patients according to disease stages and sub-sites, we showed increased survival rates for all patients.