An underdeck pontoon lift system for supporting pontoons of various sizes in a stable manner. The underdeck pontoon lift system includes a base structure, a plurality of front lifting jacks and a rear lifting jack pivotally attached to the base structure, a support bed pivotally attached to the lifting jacks, a front structure extending from the base structure, and an elevating unit for manipulating the lifting jacks. The lifting jacks preferably have an inverted U-shaped base member with a pair of support members extending upwardly, where the width of the support members is less than the width of the base member. The lifting jacks are preferably attached to cross members that extend between side members of the base structure. The support bed preferably has a rear tapered portion for assisting in the loading of a pontoon.