Gordillo was elected to another six-year term as union leader in October. She was the only candidate and there was not a single dissenting vote.
For years, she has beaten back attacks from union dissidents, political foes and journalists who have seen her as a symbol of Mexico's corrupt, old-style politics. Rivals have accused her of corruption, misuse of union funds and even a murder, but prosecutors who investigated never brought a charge against her.
She was expelled from Pena Nieto's Institutional Revolutionary Party in 2006 for supporting other parties' candidates and the formation of her own New Alliance party.
The overhaul was Pena Nieto's first major proposal since taking office Dec. 1 and is considered a political blow to Gordillo, who has played the role of kingmaker for many Mexican politicians.
She was conspicuously absent from Monday's announcement and offered no immediate reaction.
Gordillo has previously said she will fight to make sure the rights of teachers aren't hurt by the reform.