We consider a family of metric generalized connections on transitive Courant algebroids, which includes the canonical Levi-Civita connection, and study the flatness condition. We find that the building blocks for such flat transitive Courant algebroids are compact simple Lie groups. Further, we give a description of left-invariant flat Levi-Civita generalized connections on such Lie groups, which, in particular, shows the existence of non-flat ones.