Rays shortstop Wander Franco has been placed on administrative leave through June 1 amid an ongoing investigation into an alleged relationship with an underage girl, a source confirmed to The Post.

The Rays open their season Thursday at home against the Blue Jays.

Major League Baseball and the MLB Players Association agreed on the clerical maneuver that removes Franco from the 40-man roster, as first reported by the Tampa Bay Times.

Franco has not been with the team since August after the allegations of a sexual relationship with a 14-year-old girl first came to light, and he has not been charged with a crime.

He finished the 2023 season on administrative leave after being placed on the list Aug. 22, and did not appear at spring training.

Franco has been staying in his native Dominican Republic, according to the Associated Press, where he is under investigation for allegations of sexual and psychological abuse.

He is required to make monthly court appearances as the investigation continues.

The Tampa Bay Times reported this administrative leave could be extended if there is no update in the investigation by the deadline.

MLB is “likely to wait” until after the investigation to levy any discipline, per the Associated Press report.

This maneuvering came hours before Opening Day since the Rays had to get their roster in place for their season opener.

There had been questions about whether Franco would remain on administrative leave or be placed on the restricted list since that affects pay.

Since he’s on the administrative list, Franco will continue to be paid.

Franco is set to make $2 million this year, the last year with a relatively low base during his 11-year, $182 million contract he signed with the team in 2021.

He is still owed approximately $175 million.

Franco, 23, emerged as arguably the Rays’ best player, posting an .819 OPS last season while hitting 17 homers, tallying 58 RBIs and adding 30 stolen bases.

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