MTA “Overtime King” Thomas Caputo, who had pleaded not guilty to allegedly conspiring with coworkers to collect massive amounts of illegitimate pay, has reversed course and copped a plea deal, his lawyer told The Post on Tuesday.

Caputo, a former LIRR track inspector, is now seeking a court hearing as early as July 20 to reverse his earlier plea, said Audrey Strauss, the US Attorney for the Southern District, in a letter Tuesday to Judge Paul Engelmayer.

Meanwhile, one of Caputo’s alleged cohorts, ex-Long Island Rail Road track foreman Joseph Balestra, who also pleaded not guilty to the charges in February, now “intends to plead guilty” but has requested time “to confirm the effect of the plea on his pension,” Strauss said.

Balestra and Caputo are accused with three others of reaping thousands of dollars in pay for time they did not work by taking advantage of what the MTA Inspector General’s Office has called an “honor system” for reporting hours.

Caputo, now 57, earned $461,000 in 2018 alone — more than any other MTA employee that year, including the agency’s chairman, The Post reported in 2019.

Those earnings included an unfathomable 3,864 overtime hours, averaging out to 10 hours of OT for all 365 days of the year, according to prosecutors.

Investigators allege Caputo was nowhere near work on multiple occasions while collecting OT — including at least two times he spent bowling in Suffolk County.

The group of LIRR hacks allegedly “worked together to fraudulently claim pay for hours they did not work by … covering for one another’s absences,” court papers say.

Caputo retired in 2019 amid the probe but has continued to receive pension payments from the MTA — including $144,000 in the year leading up to his arrest in December.

Balestra, 51, resigned from the job June 22, MTA officials said.

Balestra’s lawyer did not return a request for comment.