The 21-year-old, who was crowned winner of the singing competition earlier this week, had eight operations during the course of Idol due to chronic kidney problems.
The singer endured "immense pain" during the show because of kidney stones that are too big to pass through his system, TMZ reports.
Doctors inserted a stent into Phillips's kidney seven weeks ago as a temporary fix, but this did little to relieve the pain.
His doctor even advised him to quit American Idol to get surgery when he returned home to Georgia.
The surgery will now take place on Tuesday afternoon, followed by a six-week recovery period.
An American Idol executive has offered the use of his Malibu mansion to Phillips and his parents for the entire recovery period.
Speaking of his condition, Phillips told Digital Spy: "My right kidney just isn't kind of functioning and I need a little help with that so kind of have to get that fixed up pretty soon.
"I'll get surgery soon - not just quite yet, but soon. I believe I should be 100% by the time the tour starts, so I won't miss anything."
Watch Phillip Phillips perform his winner's song 'Home' on American Idol below: