ATLANTA — The perpetually penalized Yankees need to choose wisely in the draft, hurt often by their spending and winning habits.

To that end, they are gambling that Dax Kilby will be a late first-round find.

With the 39th overall pick on Sunday, technically in the Competitive Balance Round A portion, the Yankees selected the shortstop out of Newnan High School in Georgia.

Kilby, who will have to be signed away from a commitment to Clemson, is a 6-foot-2, 190-pound lefty swinger who reportedly hit .495 in his senior season, when he led his school to a Georgia state championship.

The Yankees — whose original pick was 29th because they lost in the World Series, and who saw that spot set back 10 spots because they exceeded the threshold of the Competitive Balance Tax by $40 million last season — have to maximize their choices in part because they are further back in the draft and in part because they will not choose as often as others. 

They also were stripped of two picks and did not own a second-round pick altogether because they signed Max Fried, to whom the Braves had extended a qualifying offer.

They have $5,383,600 to distribute as signing bonuses to their draft picks — the least in baseball.

The Yankees were set to make two Sunday selections, their next at pick 103rd overall — the second-to-last pick in the third round. Rounds 4-20 will be held on Monday.

Last year, the Yankees used their first-round selection on righty Ben Hess, who owns a 4.08 ERA with 80 strikeouts in 53 innings with High-A Hudson Valley.

The Yankees have trended toward using their top picks on position players over the past several years, selecting just one pitcher — Hess — in the first round since 2018.

After taking Clarke Schmidt in 2017, the Yankees have gone with Anthony Seigler (’18), Anthony Volpe (’19), Austin Wells (’20), Trey Sweeney (’21), Spencer Jones (’22), George Lombard Jr. (’23), Hess and now Kilby.