British publishers initially rejected the book because it didn't include European aspects.
Makumbi will take home $165,000 for her debut novel, Kintu and is one of eight writers to win a Windham Campbell Prize.
"This prize for me is like having been working without pay for a long time and then someone comes a long and says, 'Will a salary for the past ten years do?' Then you're left speechless."
"I couldn't believe it, I was crying. I'd just published one book and it's been out only less than a year in America." Makumbi said on receiving the award.
And it is easy to see why she couldn’t believe it.
When Makumbi first sent Kintu to British publishers it was initially rejected because it was 'too African' and it didn't include European aspects.
"Publishers in the UK are thinking about their readers in Britain and normally when they publish African novels they prefer to publish novels that deal with Europe as well,"
"This novel had cut colonization out," Makumbi told CNN.
Makumbi was however upbeat about the book which was first published in Kenya four years ago.
"The book was sold in East Africa and it was an instant hit," Makumbi said.
Kintu is about the myths of a Ugandan family who think they have been cursed since the 18th century.
"It dates back to the 1700s before Europe arrived and the language itself is very Ugandan even though it's in English. There's quite a lot of Ugandan words. The story is told like it's spoken to Ugandans."
Windham Campbell prize is however not the first award the Uganda author, who is now based in Manchester after moving to the UK 17 years ago has won.
In 2014 she was awarded the Commonwealth Short Story Prize for her work "Let's Tell This Story Properly."
Makumbi's next book is a collection of short stories titled "Love Made in Manchester," to be released next January.