Transketolase (TK) catalyzes a reversible transfer of a two‐carbon (C2) unit between phosphoketose donors and phosphoaldose acceptors, for which the group‐transfer reaction that follows a one‐ or two‐electron mechanism and the force that breaks the C2“−C3” bond of the ketose donors remain unresolved. Herein, we report ultrahigh‐resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group‐transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme‐catalyzed non‐Kekulé diradical cofactor brings about the C2“−C3” bond cleavage/formation for the C2‐unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.