Quality of life (QoL) and individual perception of health has become a subject of great interest in Lithuania. The relationships between country residence, socio-economic status (SES), and QoL have not been well characterized among the Lithuanian urban and rural populations. The aim of the study was to assess the influence of country residence and SES on QoL in Lithuanian urban and rural population adjusting for the influence of other known determinants of QoL. The study population was randomly selected from 1193 urban and 264 rural men and women aged 45–72 years and have been filled in the self-administered the WHOQOL-100 questionnaire. The survey participation rate was 62.8%. Psychometric evaluation of the WHOQOL-100 showed good internal reliability of Cronbach’s α from 0.78 to 0.94. Multiple linear regression models were used to study the influence of country residence and SES on the WHOQOL-100 scores while adjusting for the influence of other determinants of QoL. After adjusting for the influence of these factors, country residence and SES independently influenced QoL. Rural residence negatively affected the overall QoL, psychological domain, level of independence and spirituality. Higher education level and income directly and positively influenced the WHOQOL-100 scores, while retired, unemployed and residents with chronic medical conditions had negative influence WHOQOL-100 scores. The study results conclude that country residence and SES are associated with differences in QoL among urban and rural Lithuanian population.