The rapper/producer, real name Joseph Junior Adenuga, was due to perform at the Grant Park site in Chicago, Illinois on 29 July (16) as part of the four-day music event, which runs from 28 to 31 July (16).
However, organisers for the festival announced on social media he would no longer be on the bill and announced his replacement, Chicago-area rapper Joey Purp.
"Due to ongoing Visa issues, Skepta will not be able to perform at Lollapalooza this year," they wrote. "Joey Purp has been added to the Lolla Lineup and will perform on Perry’s Stage at 2:30pm, Friday, July 29th."
Skepta hasn't commented on the cancellation himself.
This isn't the first time Skepta has had problems getting into the U.S. - visa problems forced him to drop out of the Coachella music festival in California in April (16) and several subsequent tour dates.
At the time, he wrote on Instagram, "Love to everybody that wanted to see me on tour this month, my U.S visa has been denied and I am not allowed in America right now. Still taking forward steps and forever working with God. Brb (be right back)."
It isn't clear why Skepta was denied a visa.