Forests and the forest-based sector play important roles in mitigating climate change through carbon sequestration and storage in living biomass and soil. In Europe, the forest sector is the only sector that positively affects atmospheric carbon balance. After the forest harvest, a large share of carbon is removed together with the wood. This wood carbon might be stored for centuries if in the form of long-lived wood products. In 2011, the United Nations decided that countries should account for and report carbon balance not only in forests but also in harvested wood products (HWP), followed by very general guidelines on methods for carbon accounting in HWP. The Intergovernmental Panel on Climate Change (IPCC) proposed three methodological levels called tiers for estimating carbon stock and its changes in HWP. The first reporting period revealed that countries applied different carbon accounting methods (tiers), therefore comparing the carbon budgets of HWP and the effect of climate change mitigation among different countries is difficult. In order to test the differences between carbon accounting methods proposed by the IPCC guidelines, we applied two carbon accounting methods and used different data sources in the case of Lithuania. The methods applied were the IPCC Tier 2 method (data on HWP from statistics or the literature, default half-life values, and default HWP categories) and material flow analysis, which is compatible with the IPCC Tier 3 method (material flow data on HWP, country-specific half-life values, and country-specific HWP categories). Depending on the availability of historical data from different sources for the purpose of this study, three study periods were defined: 1992–2015 Food and Agriculture Organization Corporate Statistical Database (FAOSTAT) data, 1960–1991 data from the literature, and 1940–1991 data from national statistics. The study findings show that carbon stock in HWP significantly differed when different data sources and methods were applied. The highest carbon stock in HWP (19.5 Mt) at the end of the study period was observed when FAOSTAT data from 1992–2015 were used and the Tier 3 method was applied. The lowest carbon stock in HWP (11.2 Mt) at the end of the study period was observed when data from national statistics from 1940–1991 were used and the Tier 2 method was applied. The carbon inflow into the pool of HWP in all cases was estimated to be 40% higher when material flow analysis was applied compared to the IPCC default (Tier 2) method. These findings suggest that in general it is more reasonable to apply the Tier 3 method for carbon accounting of HWP in Lithuania.