Deviations in rainfall duration and timing are expected to have wide-ranging impacts for people in affected areas. One of these impacts is the potential for increased levels of conflict and accordingly, researchers are examining the relationship between climate variability and conflict. Thus far, there is a lack of consensus on the direction of this relationship. We contribute to the climate variability and conflict literature by incorporating Markov transitional probabilities into panel logit models to analyze how monthly deviations in rainfall affect the likelihood that a grid cell transitions to an above average level of conflict in Sub-Saharan Africa. To control for differences in seasons across the continent, we model this relationship for each of the regions of Sub-Saharan Africa separately – East, Central, West, and Southern. We find significant seasonal and regional effects between rainfall and the probability that a grid cell transitions from a state of peace to a state of conflict. In particular, above average rainfall is associated with a higher likelihood of transitioning into conflict during the dry season. Further, each region has specific months—primarily those associated with prime crop harvest periods—where variations in rainfall significantly influence conflict. We also find regional variations in the linkage between rainfall and conflict type related to the types of conflict that predominate in particular regions of Sub- Saharan Africa. These findings are important for policymakers because they suggest additional law enforcement and/or peacekeeping resources may be needed in times of above average rainfall. Policies that provide financial support for farmers or other sectors, such as mining, that are impacted by rainfall patterns may also be a useful strategy for conflict mitigation.