Harry Thomas Jr. resigned Thursday night, hours after he became the first sitting D.C. Council member to be charged with a felony, when federal prosecutors accused him of embezzling more than $350,000 in government funds and filing false tax returns.

In a statement issued shortly after 8 p.m., Thomas said: “I am resigning my position as a member of the Council effective immediately. I made some very serious mistakes and exhibited inadequate and flawed judgment. I take full responsibility for my actions. I am truly sorry.”

A plea hearing in the case has been scheduled for Friday morning before U.S. District Judge John D. Bates, and in his statement, the Ward 5 Democrat said he would plead guilty to two federal crimes.

Thomas is the first member of the D.C. Council to resign under duress since the District’s home rule government was first seated, in 1975.

Neither Thomas nor his attorneys would comment further Thursday. William Miller, a spokesman for U.S. Attorney Ronald C. Machen Jr., declined to comment on the court filing.

Thomas, the 51-year-old son of a former Ward 5 council member, is alleged to have steered the money, intended for youth sports programs, through intermediaries to pay for personal expenses that included an Audi sport-utility vehicle and golf trips.

The probe has its roots in suspicions first leveled during Thomas’s 2010 reelection campaign by his Republican opponent about his fundraising for a nonprofit group he founded. The District’s attorney general at the time, Peter Nickles, initiated a probe of the charity, called Team Thomas. Nickles’s successor, Irvin B. Nathan, first outlined the graft allegations in a civil suit in June; he referred the case to the U.S. attorney’s office for criminal charges.

At the time, Thomas indicated that he had done nothing wrong. “There is no settlement that I would make that would imply that there was some wrongdoing on my part,” Thomas said the day Nathan filed his lawsuit. But about six weeks later, Thomas agreed to a settlement requiring him to repay the city $300,000. He again denied any malfeasance, saying that he settled “to ensure that the trust the public has placed in me is maintained and honored.”

Yet it became clear in recent months that federal authorities were aggressively pursuing Thomas. FBI and IRS agents raided Thomas’s home last month and seized several personal items, including an SUV.

The federal probe came after editorials in The Washington Post on spending practices involving the council member and Team Thomas.

On Thursday, prosecutors filed a four-page charging document that alleges Thomas embezzled $353,500 between April 2007 and February 2009. He is also accused of filing false tax returns in 2007, 2008 and 2009. The charging papers allege that he underreported his income in those years by a total of $346,000. Prosecutors are seeking the forfeiture of a 2008 motorcycle and a 2008 Chevrolet Tahoe connected with the case, according to the charging papers.

The federal charges came in a “criminal information,” a type of charging document that can only be filed with the defendant’s consent and generally signals that a plea deal has been reached.

If Thomas proceeds with guilty pleas, he faces a maximum sentence of 10 years in prison and a fine of $250,000 on the theft charge and could face up to three years in prison and a $250,000 fine for filing a false tax return. However, under federal guidelines, Thomas is likely to face a much more lenient sentence.

The Thomas case is one of three known federal investigations involving sitting District politicians. Authorities continue to probe Mayor Vincent C. Gray’s 2010 campaign, including allegations of illegal cash payoffs, and the D.C. elections board referred D.C. Council Chairman Kwame R. Brown’s 2008 at-large campaign for a federal review of unreported transactions and other irregularities.

D.C. politicians greeted the Thomas charges with somber words. But several expressed hope that the investigation’s resolution will allow officials to begin moving out from under a cloud of public suspicion that has hung over city government for nearly a year.

“Fundamentally, what is at issue here is the need of the council and government to restore the public trust,” said council member Phil Mendelson (D-At Large). “We cannot do that as long as this matter is unresolved.”

In a statement Thursday, Gray (D) had urged Thomas to resign.

“While everyone is presumed innocent until proven otherwise, those who violate the public’s trust must be held accountable for their actions,” Gray said.

Brown (D) said in a phone interview Thursday night after Thomas made his announcement: “I am deeply saddened by what has taken place. It is a somber day for the residents, but nothing is to be preferred before justice.”

Last week, Thomas began meeting with friends to apologize for the allegations hanging over his head. He told them that he expected to enter a guilty plea this week and to get a three-year prison sentence, according to friends of his.

Federal prosecutors and Thomas’s attorney have spent the past few days negotiating an agreement in the case.

Sources familiar with the plea negotiations said guidelines suggest a prison sentence in the range of three or four years. But at sentencing, Thomas will be able to argue for less time or even probation, the sources said, speaking on the condition of anonymity because of the sensitivity of the talks and because they were not authorized to discuss them.

Thomas’s resignation has been a key part of the plea talks. It is rare but not unprecedented for federal prosecutors to require the resignation of an elected official in a public corruption cases. Under D.C. law, a sitting official convicted of a crime is removed from office only when incarcerated for a felony.

The new ethics package recently passed by the D.C. Council includes a provision to immediately expel members who have been convicted of felonies. However, that provision would not become effective without a change to the city charter. Such a change requires a voter referendum, which could not be held earlier than November, or an act of Congress, which could take longer.

There is no city law barring someone from running for office after a felony conviction. Should the charter amendment contemplated in the ethics bill succeed, a person would be eligible for council office only if he or she “has not been convicted of a felony while holding the office.” By resigning before entering a plea, Thomas appears to remain eligible for office.

It will be months before there is new representation for residents in Ward 5, which encompasses most of the Northeast Washington quadrant west of the Anacostia River.

Council member Vincent B. Orange (D-At Large), who held Thomas’s seat for eight years, said Thursday that he would “fill the leadership void” until a new member is elected.

Under city law, a special election must be held on the first Tuesday at least 114 days after a vacancy is declared. There is no provision for an interim appointment for ward council members.

Once the D.C. Board of Elections and Ethics has been officially notified of Thomas’s resignation, it has five days to declare a vacancy. If that declaration happens at the board’s regularly scheduled meeting Wednesday, a special election would take place May 8.

Staff writers Tim Craig and Nikita Stewart contributed to this report.