A balloon folding system specifically configured to reduce a side branch balloon of a bifurcated balloon catheter assembly includes a die that defines at least one chamber for receipt of the sidebranch balloon, and at least one pin sized to fit into the chamber and reduce the balloon to a substantially flattened state. The system also may include a housing for the reduction and folding of a primary branch balloon. The system is configurable to fold and reduce both branches simultaneously or separately.