The Royal Swedish Academy of Sciences said the two researchers had made key contributions to experiments showing that neutrinos change identities.
"The discovery has changed our understanding of the innermost workings of matter and can prove crucial to our view of the universe," the academy said.
Kajita is director of the Institute for Cosmic Ray Research and professor at the University of Tokyo.
McDonald is a professor emeritus at Queen's University in Kingston, Canada.
The winners will split the 8 million Swedish kronor (about $960,000) prize money. Each winner also gets a diploma and a gold medal at the prize ceremony on Dec. 10.
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