CBC News has spoken to Thibeault and confirmed the news. He is expected to release a statement with Wynne's office at 10 a.m. ET.
The federal NDP is also expected to react shortly.
Thibeault stepped down as the federal NDP's caucus chair earlier this fall, citing family reasons.
He was first elected as a federal MP six years ago, in the 2008 election. As of October, he had served long enough federally to be eligible for the MP pension plan.
Thibeault's resignation follows Friday's announcement by NDP deputy leader Libby Davies that she will not run in the next election.
Offer to step aside?
Thibeault's announcement comes after a top Ontario Liberal party official refuted a claim by their recent Sudbury candidate that he was asked not to run in an upcoming byelection in exchange for an appointment.
Andrew Olivier, who narrowly lost to now-resigned NDP MPP Joe Cimino in last June's election, said he was asked by high-ranking Liberal officials — including campaign director Pat Sorbara and Premier Kathleen Wynne — to step aside.
Olivier said one party official told him that if he didn't run they would "see what was in it" for him.
Sorbara said the claim that "anything was offered in exchange for any action is categorically false," while Wynne denied that she or any members of her party promised an appointment.
Wynne said that, while she reached out to Olivier to let him know the Liberals had another candidate in mind, there were no "specific offers" made.
Olivier said he is not seeking the nomination for the byelection, which has yet to be called.
The Progressive Conservatives have asked the Ontario Provincial Police to look into the allegations.
The provincial NDP directed the allegations to Elections Ontario, saying that under the Election Act it is an offence to promise a job or appointment to induce a person to withdraw their candidacy.