Fossilization in amber is unique in preserving specimens with microscopic fidelity; however, arthropod inclusions are rarely examined beyond the exoskeleton as this requires destructive sampling when traditional techniques are used. We report the first complete, digital 3D, non-destructive reconstruction of the anatomy of an insect fossil, a specimen of Mengea tertiaria embedded in a 42-Ma Baltic amber. This was made possible using Synchrotron micro-CT. The species belongs to the stem group of the phylogenetically enigmatic and extremely specialized Strepsiptera. Most internal structures of the fossil are preserved, but small parts of the lumen had decayed due to incomplete infiltration of the resin. Data on internal organs provided additional information for resolving phylogenetic relationships. A sister group relationship between Mengea and all extant lineages of the group was confirmed with characters previously not accessible. The newly gained information also yielded some insights in the biology of Mengea and the early evolutionary history of Strepsiptera. The technique has a tremendous potential for a more accurate interpretation of diverse fossil arthropods preserved in ambers from 130 Ma to the present.