The branching pattern of a tree determines the efficiency of light interception and carbon assimilation. Pruning can modify the branching pattern, as a result of changes in physiological and environmental conditions, and ultimately pruning can have major effects on yield. For one of the major tropical tree crops, cocoa (Theobroma cacao), very little is known about branching response to pruning. To address this knowledge gap we performed a pruning experiment on young cocoa trees in Cote d' Ivoire. We applied five treatments: two heading treatments (the removal of the terminal apex or 66% of a branch) and two thinning treatments (the removal of 1 or 2 primary branches) and one unpruned control. The branching pattern of the primary branches was described by the number, position, and length of lateral branches right after pruning, and the same observations were repeated after a cycle of leaf production. The probability of branching and the length of lateral branches along a primary branch, in pruned and unpruned conditions, was analyzed using generalized mixed effect models. In unpruned conditions, the probability of branch presence was higher towards the middle of the primary branches and lower at the extremes. Branch length decreased going from the base to the tip of a primary branch. After one cycle of leaf production, new branches emerged preferentially on the distal section of a branch, but probability of branch emergence was reduced by the presence of other lateral branches. Pruning increased the probability of branch emergence mostly towards the tip of a branch, with heavy heading having the strongest effect. By contrast, heavy thinning increased branch emergence also toward the base of the branch. Our results can be applied to improve formation pruning, as this may trigger branching in different part of the crown, depending on the form of pruning. Our study also assists the development of three-dimensional tree models that could further our understanding of the impact of pruning on cocoa growth and productivity.