Non-planar semiconductor devices having self-aligned fins with top blocking layers and methods of fabricating non-planar semiconductor devices having self-aligned fins with top blocking layers are described. For example, a semiconductor structure includes a semiconductor fin disposed above a semiconductor substrate and having a top surface. An isolation layer is disposed on either side of the semiconductor fin, and recessed below the top surface of the semiconductor fin to provide a protruding portion of the semiconductor fin. The protruding portion has sidewalls and the top surface. A gate blocking layer has a first portion disposed on at least a portion of the top surface of the semiconductor fin, and has a second portion disposed on at least a portion of the sidewalls of the semiconductor fin. The first portion of the gate blocking layer is continuous with, but thicker than, the second portion of the gate blocking layer. A gate stack is disposed on the first and second portions of the gate blocking layer.