Knowledge about the extent of the COVID-19 mortality burden is important to inform policy-making decisions. To gain greater insights into the population health impact of COVID-19 mortality, Years of Life Lost (YLL) can be estimated. We aimed to determine YLL linked to COVID-19 over the first two years (March 2020–March 2022) of the pandemic in Cyprus, by areas, and by age and sex. COVID-19 YLL was estimated by multiplying COVID-19 mortality counts by age-conditional life expectancy from the 2019 Global Burden of Disease life table. COVID-19 accounted for 16,704 YLL over the first two years of the pandemic—approximately 18.5 years lost per individual who died due to COVID-19 and 1881 YLL per 100,000 population. YLL per 100,000 was higher among males compared to females (2485 versus 1303 per 100,000) and higher among older than younger individuals. COVID-19 deaths and YLL per 100,000 were higher in high population-dense areas of Cyprus, such as Limassol. Continued evaluations of COVID-19 YLL are needed to inform on the proportionate population impact of COVID-19, over time and across areas of Cyprus.