After a decade of fertility decline, Ghana’s fertility and the level of unmet need for contraception stalled in mid-transition in the late 1990s. Although the literature acknowledges this, the geographical patterns in unmet need have not been adequately documented. Spatial analysis of unmet need can reveal differences in usage and provision of contraceptive commodities, thereby pointing to geographical areas where contraceptive programmes should be strengthened. This study examines the geographical variation of the risk of mistimed and unwanted pregnancies between rural communities and also between urban communities of the three ecological zones of Ghana. The study also investigates if geographical differences in the risks of mistimed and unwanted pregnancies changed during the period when unmet need stalled at the national level. A multilevel regression model was applied to pooled data from the 1998 and 2003 Ghana Demographic and Health Surveys to examine the determinants of the risk of unintended pregnancies, while controlling for clustering of outcomes within communities. The results show that between the two surveys, there was no significant change in the levels of risk of mistimed and unwanted pregnancy. However, geographical heterogeneity in the risk of mistimed and unwanted pregnancy was observed, after controlling for relevant predictors. This showed concentration of mistimed pregnancies in some rural communities relative to others, and variation in the risk of unwanted pregnancies between urban communities. The results give a clear indication that bridging the inequality gap in contraceptive use requires programmes that are area-specific.