The Mets lost out on Roki Sasaki, but ended up with what they hope is a pretty good consolation prize in 17-year-old shortstop Elian Pena from the Dominican Republic, a source confirmed.

Considered by some scouts to be the next-best international free agent, Pena signed a $5 million deal with the Mets on Wednesday, the first day of the international signing period, after they initially agreed to a deal last season.

The move takes up most of the team’s $6.2 million bonus pool.

If the Mets had been able to sign Sasaki — the Japanese right-hander who has narrowed his choices to the Dodgers, Padres and Blue Jays and is expected to sign within the week — they wouldn’t have had enough money left to bring in Pena.

Pena’s bonus is the largest in franchise history, far surpassing the $2.85 million given to Venezuelan catcher Yovanny Rodriguez a year ago.

It’s also the the largest for any Latin player this year.

It’s also one of the largest bonuses in MLB history.

Listed at 5-10, the lefty-swinging Pena has impressed more at the plate than in the field.

“If you don’t get Sasaki, this will make it easier to take,’’ one American League scout said of Pena. “I’m not sure there’s anyone with more upside offensively than Pena.”

His glove needs some work, according to scouts, but he’s signed for his bat.

“You’re never sure how these guys are going to develop physically or skill-wise, but he has a swing that stands out already,’’ the scout said.

There have been early comparisons to Boston third baseman Rafael Devers for Pena, but another scout wasn’t convinced he will hit as many homers.

“He’s got power, discipline at the plate and knows how to play the game,’’ the scout said. “He’s going to be a dangerous, well-rounded hitter if all goes well.’’

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