During the closing stages of Saturday's 2-0 defeat to Manchester City in the FA Cup quarter-finals, Botman was forced to be withdrawn after suffering a knee issue.
The development was of natural concern for Eddie Howe courtesy of Botman having dealt with a knee injury earlier in the season and spent three months on the sidelines.
In that instance, the 24-year-old opted against surgery and the appearance against City at the Etihad Stadium was his 16th in a Newcastle shirt since December 16.
However, the Magpies have revealed that Botman will now miss between six to nine months after it was determined that he required an operation on an ACL injury.
A club statement read: "Newcastle United defender Sven Botman will undergo surgery next week after suffering a knee injury against Manchester City.
"Following further assessment, a scan has confirmed that he sustained an injury to his ACL during Saturday's match and he is expected to return to action within six-to-nine months.
"The Dutch centre-back initially sustained a knee injury in September 2023 and elected for a non-surgical rehabilitation plan - a decision which saw him return to action in December.
"Everyone at Newcastle United wishes Sven a full and speedy recovery."
Although Botman is uncapped at senior level, the injury rules out him of contention for the Netherlands squad at Euro 2024.
From a Newcastle perspective, it is a significant blow to their hopes of securing European football for next season, Botman having contributed two goals and two assists from his 17 Premier League appearances during 2023-24.
With 10 games remaining, the North-East outfit sit in 10th position in the top-flight standings, two points adrift of eighth-placed Brighton & Hove Albion and four behind West Ham United in seventh position.
Jamaal Lascelles, Dan Burn, Emil Krafth and Paul Dummett will now compete to replace Botman alongside Fabian Schar.