"Had an appendectomy today but Alhumdulillah (by the grace of God) feeling better. Remember me in your prayers," he tweeted, along with a picture of him in a hospital bed.
His elder brother Riaz, also a Pakistan Test cricketer, told AFP Shaheen suffered a rapid onset of appendicitis.
"Shaheen had had breakfast early Sunday and after an hour or so felt severe pain so we took him to a doctor who diagnosed appendicitis and did the surgery," said Riaz.
He has been advised to take at least a week's rest.
Shaheen is already undergoing rehab after hurting his knee in the Twenty20 World Cup final in Melbourne on November 13.
The latest surgery will likely rule him out of the Test series against England, scheduled to start in Rawalpindi on December 1.
Shaheen, Pakistan's strike bowler in all formats of the game, has 99 Test, 62 ODI and 58 Twenty20 international wickets from a career that started 2018.
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