Magnetic skyrmions have so far been treated as two-dimensional spin structures characterized by a topological winding number. However, in real systems with the finite thickness of the device material being larger than the magnetic exchange length, the skyrmion spin texture extends into the third dimension and cannot be assumed as homogeneous. Using soft x-ray laminography, we reconstruct with about 20-nanometer spatial (voxel) size the full three-dimensional spin texture of a skyrmion in an 800-nanometer-diameter and 95-nanometer-thin disk patterned into a 30× [iridium/cobalt/platinum] multilayered film. A quantitative analysis finds that the evolution of the radial profile of the topological skyrmion number is nonuniform across the thickness of the disk. Estimates of the micromagnetic energy densities suggest that the changes in topological profile are related to nonuniform competing energetic interactions. Our results provide a foundation for nanoscale metrology for spintronics devices using topology as a design parameter.