Topological insulators (TIs) represent a class of matter associated with unique electronic and spin properties held by chiral and massless Dirac fermions. The lattice mismatch between the HgTe layer and the CdTe substrate, which is the reason for the TI properties in HgTe/CdTe, is less than 0.4%. Measuring it necessitates an extremely sensitive technique, while a nanometric spatial resolution is mandatory to characterize the strain gradient across the layers. In this letter, we demonstrate the use of nano-beam precession electron diffraction to map the strain of the whole stack, thus experimentally addressing the strain distribution in such systems. Strain maps with a precision of 0.03% and a spatial resolution of 1.9 nm show good agreement with finite element simulations of the expected strain. Strain values and gradients are within the intervals predicted to yield the TI properties of the material. © 2017 Author(s).