Nanojunctions promise to provide higher charge transport efficiencies and less costly solar cell fabrication methods. We report a three-dimensional (3D) solar cell structure based on interdigitated nanojunctions formed with the tips of n-type ZnO nanocones embedded in a p-type polycrystalline (PX) CdTe film. This 3D nanocone tip-film cell, without optimization, enabled 3.2% power conversion efficiency, higher than that produced by a planar solar cell fabricated using the same materials. Reducing CdTe grain size and enriching the grain boundaries with chlorine improved the conversion efficiency for the tip-film structure. This higher conversion efficiency is attributable to improved charge transport in the nanojunction due to a combination of the high electric field generated in the CdTe and the utilization of the small junction area. The high field facilitates the extraction of minority carriers from the photoactive layer to the small junction region, while the use of the small junction area reduces the total electron recombination loss. The improved carrier transport in the nanocone tip-film junction implies that nanocone-based photovoltaic solar cells are capable of tolerating the imperfect materials produced using low-cost fabrication methods.