Using a map overlay procedure in a Geographical Information System environment, we quantify and map major land use and land cover (LULC) change patterns in Uganda period 1990–2005 and determine whether the transitions were random or systematic. The analysis reveals that the most dominant systematic land use change processes were deforestation (woodland to subsistence farmland—3.32%); forest degradation (woodland to bushland (4.01%) and grassland (4.08%) and bush/grassland conversion to cropland (5.5%) all resulting in a net reduction in forests (6.1%). Applying an inductive approach based on logistic regression and trend analyses of observed changes we analyzed key drivers of LULC change. Significant predictors of forest land use change included protection status, market access, poverty, slope, soil quality and presence/absence of a stream network. Market access, poverty and population all decreased the log odds of retaining forests. In addition, poverty also increased the likelihood of degradation. An increase in slope decreased the likelihood of deforestation. Using the stock change and gain/loss approaches we estimated the change in forest carbon stocks and emissions from deforestation and forest degradation. Results indicate a negligible increase in forest carbon stocks (3,260 t C yr-1) in the period 1990–2005 when compared to the emissions due to deforestation and forest degradation (2.67 million t C yr-1). In light of the dominant forest land use change patterns, the drivers and change in carbon stocks, we discuss options which could be pursued to implement a future national REDD plus strategy which considers livelihood, biodiversity and climate change mitigation objectives.