Neer’s classification for proximal humerus fractures (PHFs) uses 10 mm and 45° thresholds to distinguish displaced fragments. While this system was originally developed referencing 2D X-rays, fracture displacements occur in three dimensions. Our work aimed to develop a standardized and reliable computerized method for measuring PHF 3D spatial displacements. CT scans of 77 PHFs were analyzed. A statistical shape model (SSM) was used to generate the pre-fracture humerus. This predicted proximal humerus was then used as a “layer” to manually reduce fragments to their native positions and quantify translation and rotation in three dimensions. 3D computerized measurements could be calculated for 96% of fractures and revealed that 47% of PHFs were displaced according to Neer’s criteria. Valgus and varus head rotations in the coronal plane were present in 39% and 45% of cases; these were greater than 45° in 8% of cases and were always associated with axial and sagittal rotations. When compared to 3D measurements, 2D methods underestimated the displacement of tuberosity fragments and did not accurately assess rotational displacements. The use of 3D measurements of fracture displacement is feasible with a computerized method and may help further refine PHF analysis and surgical planning.